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Title: large language model for vulnerability detection and repair: literature review and the road ahead.

Abstract: The significant advancements in Large Language Models (LLMs) have resulted in their widespread adoption across various tasks within Software Engineering (SE), including vulnerability detection and repair. Numerous recent studies have investigated the application of LLMs to enhance vulnerability detection and repair tasks. Despite the increasing research interest, there is currently no existing survey that focuses on the utilization of LLMs for vulnerability detection and repair. In this paper, we aim to bridge this gap by offering a systematic literature review of approaches aimed at improving vulnerability detection and repair through the utilization of LLMs. The review encompasses research work from leading SE, AI, and Security conferences and journals, covering 36 papers published at 21 distinct venues. By answering three key research questions, we aim to (1) summarize the LLMs employed in the relevant literature, (2) categorize various LLM adaptation techniques in vulnerability detection, and (3) classify various LLM adaptation techniques in vulnerability repair. Based on our findings, we have identified a series of challenges that still need to be tackled considering existing studies. Additionally, we have outlined a roadmap highlighting potential opportunities that we believe are pertinent and crucial for future research endeavors.

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A Literature Review on Automated Code Repair

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• First Online: 10 January 2022
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• T. Mamatha 11 ,
• B. Rama Subba Reddy 12 &
• C. Shoba Bindu 11  

Part of the book series: Lecture Notes in Networks and Systems ((LNNS,volume 237))

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Automated code debugging has engaged researchers owing to its potential to minimize repair costs. To reduce the developer’s load, bug correcting, and extracting methods are widely used to demonstrate as problem results for productive fixing and nurturing the work product in the last few years. We analyzed several automated tools, techniques, and strategies that applied in different applications, languages which gave tremendous results in some cases, so we try to grab the works that happened. Our survey on code repair tools will help the developers in locating the accurate position where the bug occurs, this can significantly reduce the cost of software development. In this paper, we studied some tools for automated correction and localization of tools from 2001 and analyzed the effectiveness of the tools. We show the results of our survey in Table 1 of Fault Localization tools and Table 2 of Fault Correcting. And the graph shows the scenario of automated tools day by day and its usage. For correction tools we concentrated on parameters like Bugs Reported, Bugs corrected, Time to correct the bugs, LOC used, and finally the outcome of the tool. This survey helpful for the developers in choosing the appropriate tool.

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Mamatha, T., Reddy, B.R.S., Bindu, C.S. (2022). A Literature Review on Automated Code Repair. In: Gunjan, V.K., Zurada, J.M. (eds) Proceedings of the 2nd International Conference on Recent Trends in Machine Learning, IoT, Smart Cities and Applications. Lecture Notes in Networks and Systems, vol 237. Springer, Singapore. https://doi.org/10.1007/978-981-16-6407-6_23

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A systematic review of anterior cruciate ligament primary repair rehabilitation

George jm. hourston.

a Department of Trauma and Orthopaedics, Addenbrooke's Hospital, Cambridge, UK

Hadyn KN. Kankam

b Department of Surgery, St George's University Hospitals NHS Foundation Trust, London, UK

Stephen M. McDonnell

Rehabilitation after surgery of the injured anterior cruciate ligament (ACL) is crucial for satisfactory outcomes. Many trials have investigated this process after ACL reconstruction. The treatment of acute ACL ruptures with a repair technique has recently regained interest, although very little information is available about appropriate rehabilitation for such patients. The objective of this review was to evaluate studies on rehabilitation following ACL repair.

A systematic review of the literature following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted for patients undergoing a rehabilitation programme after ACL repair. The review has been registered on the International Prospective Register of Systematic Reviews (PROSPERO, Registration number: CRD42020173450). Elements of rehabilitation care we included in our strategy are postoperative bracing, home-based rehabilitation, strengthening exercises, proprioception and neuromuscular training. We searched PubMed, CINAHL, EMBASE, and the Cochrane Library for randomised trials of any form investigating rehabilitation protocols after repair of the injured ACL. Two reviewers independently assessed eligibility of trials.

No trials were included. Available literature of lower evidence was included for discussion.

Conclusions

No information is available from randomised trials to indicate whether there is any difference between rehabilitation protocols for patients who have undergone primary ACL repair.

1. Introduction

Anterior cruciate ligament (ACL) injury is one of the most prevalent knee injuries among young athletes. 1 Most patients with acute ACL injuries are younger than 30, and such injuries therefore result in early onset osteoarthritis. 2 This posttraumatic osteoarthritis has a significant associated morbidity and healthcare cost. 3 In the United States alone, there are estimated to be between 120,000 and 400,000 ACL reconstructions per year. 4 Fixed object high-impact rotational landing sports such as gymnastics and obstacle course racing as well as athlete-to-athlete contact sports are thought to result in the highest rates of ACL injury. 5 The current gold standard of treatment for ACL rupture is reconstruction performed soon after injury to limit further meniscal or cartilage damage. 4

Repair of the deficient ACL was first described by Robson in 1895. 6 This technique avoids donor site morbidity associated with reconstruction, and is thought to better preserve native biomechanics and proprioception. 4 ACL repair had fallen out of favour since its popularity in the 1970s and 1980s due to high failure rates. 7 , 8 , 9 However, more recently it has been noted that ACL repairs of mid-substance ruptures are associated with poor tissue quality and poor healing environments; whereas more proximal avulsions off the femoral footprint may have better outcomes of repair. 10 , 11

Physical rehabilitation for patients following any ACL injury and surgery essential for return to an active lifestyle. Post-operative care for these patients remains heterogenous. Various outcome measures are used by different centres to assess rehabilitative progress of the post-operative ACL injured knee. These measures include the visual analog scale (VAS) for pain; the international knee documentation committee (IKDC) questionnaire which is a knee-specific subjective patient-reported outcome measure; the knee outcome survey activities of daily living scale (KOS-ADLS); the ACL quality of life (ACL-QOL) questionnaire; the Tegner and Lysholm activity scales; the Cincinnati knee score which covers the domains of pain, swelling, function and activity-level; the KT1000 and KT2000 arthrometers, which are knee laxity testing devices; the Cybex 6000 isokinetic dynamometer measuring knee flexor strength; and the more pragmatic single-limb hop test. Other measures used in some series include early return to function or early return to sport.

The safety and efficacy of rehabilitation protocols has been studied extensively following reconstruction surgery, however very little data has been published evaluating rehabilitation protocols post-ACL repair. 12 , 13 , 14 The aim of this review is to determine whether there is any evidence to help direct orthopaedic surgeons towards appropriate rehabilitation techniques for their ACL repair patients.

A systematic review of the literature following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted for patients undergoing a rehabilitation programme after ACL repair. We searched PubMed, CINAHL, EMBASE, and the Cochrane Library for randomised trials of any form investigating rehabilitation protocols after repair of the injured ACL. Included search terms were “ACL”, “anterior cruciate ligament”, “repair”, “rehabilitation”, “random∗ trial” and “clinical trial”. Search strategy shown in Appendix 1 . PROSPERO registration: CRD42020173450.

2.1. Inclusion and exclusion criteria

The level of evidence required for inclusion was determined based upon recommendations by the Centre for Evidence-based Medicine. 15 This included high-quality randomised controlled trials (Level-I) or lesser quality randomised controlled trials and prospective comparative studies (Level-II). Lower levels of evidence such as case-control studies, retrospective studies, and case series were excluded.

Study selection flow diagram is shown in Fig. 1 . Two reviewers independently selected the trials that were eligible to be included in the systematic review. Any disagreement was resolved by discussion.

Study selection flow diagram.

No Level I–II studies included. Non-randomised and retrospective series were discussed to present the relevant available literature.

4. Discussion

This review has highlighted the inadequacy of data available to orthopaedic surgeons when implementing rehabilitation protocols following ACL repair surgery. Indeed to our knowledge, no attempt yet has been made to address this issue with a randomised controlled study. The literature is abundant with equivalent studies following ACL reconstruction, however given the reported advantages of proprioception and more physiological knee biomechanics in repaired compared with reconstructed ACL injured knees, appropriate rehabilitation techniques should be investigated. In order to validate accelerated rehabilitation protocols and early return to sports further evidence is needed.

ACL repair, rather than reconstruction, has gained favour in recent years with a limited amount of evidence to support its outcomes. Some authors are opting for arthroscopic primary repair of proximal ACL tears with at least good tissue quality, but suggest the technique is contra-indicated in mid-substance or chronic tears with poor tissue quality. 16 Indeed novel techniques are emerging for the repair of ACL tears including dynamic intraligamentary stabilization (DIS) which has been shown to achieve good functional recovery, with failure rates ranging between 4% and 13.6%. 17 , 18 An Austrian group reported on a high overall complication rate of 57.9% among the fifty seven patients they followed up after DIS in primary ACL repair. 19

Some studies have reported on their rehabilitation protocol following ACL repair, although no study has specifically investigated the rehabilitation itself. Büchler et al. give a thorough account of their post DIS rehabilitation protocol in five phases which have been summarised below in Table 1 17 However, the authors did not specify the type of brace used and did not clarify when use of the brace could be discontinued, although it appears this was only used as an adjunct to their Phase 1 (day 0–4). Murray et al. also report on their rehabilitation protocol in the Bridge-Enhanced Anterior Cruciate Ligament Repair (BEAR) study. 20 This is summarised in Table 2 . Included for comparison in Table 3 is a summary the evidence-based post-ACL reconstruction rehabilitation guideline developed by the MOON Group (Multicentre Orthopaedic Outcomes Network). 21

Table 1

Büchler et al. (2016) Rehabilitation protocol following ACL repair with DIS.

∗for patients with concomitant meniscal repair, partial weight bearing with 15 kg was instructed for six weeks.

(Brace type not specified. Use of brace beyond Phase 1 not specified.).

Table 2

Murray et al. (2019) Rehabilitation protocol following Bridge-Enhanced ACL Repair.

All patients were provided with a cold therapy unit (IceMan; DJO Global) for postoperative use.

Table 3

Wright et al. (2015) Rehabilitation protocol following ACL Reconstruction (MOON Guidelines) .

(specific exercise suggestions have been excluded but are available in the guidelines).

These studies have demonstrated their rehabilitation methods including postoperative bracing, weight-bearing, and strengthening techniques, however their rationale for choosing such protocols after ACL repair is undisclosed. The rationale for dividing the rehabilitation protocols into distinct phases and the variation in the timing of these phases is also not examined in any study. Whether these phases have relevance to the progression of tissue healing or changes in the inflammatory profile of the synovial fluid environment may be an important topic yet to be elucidated. Comparison of rehabilitation phases following ACL repair with rehabilitation phases following ACL reconstruction may be of little value, given that the strength of the healing ligament is not a consideration in the rehabilitation of ACL reconstruction patients. Surgical techniques are being re-developed, and more technological advances including biological supplementation of repair with bio-scaffolds and stem cells are being explored. 22 We feel that the resurgence of technical innovation in this field should be matched by a scrutinous examination of rehabilitation techniques, and that home-based rehabilitation, proprioception and neuromuscular training should also be evaluated in ACL repair studies, as they have been in trials reporting outcomes following ACL reconstruction.

Furthermore, it is clear that protocols for rehabilitation following primary repair of the ACL may need to be modified according to whether concomitant injuries to other ligamentous structures occurred at the time of injury, or if other procedures to repair such concomitant injuries are carried out at the time of the primary ACL repair. For example, Büchler et al. described an enhanced protocol with fixed extension in a brace for four days post-operatively followed by a period of partial weight bearing for patients in their cohort who had additional sutured meniscal lesions as well as primary repair of the ACL. 17 Murray et al. adapted their rehabilitation protocol in patients who had concomitant meniscal repair by further restricting the locking hinge brace to a range of motion of only 0–40° for four weeks post-operatively rather than 0–50° for two weeks post-operatively in patients with isolated ACL repair. 20 Details of these rehabilitation protocol adaptations are given in Table 1 , Table 2 One treatment goal in primary repair of the ruptured ACL is to restore joint mechanics and preserve other soft tissue structures in the knee including the menisci. Adjustments made to rehabilitation protocols following repair of the ruptured ACL according to other soft tissue injury and surgery may therefore be critical to patient outcomes. There is no compelling evidence from this literature review to suggest any method or adaptation is superior.

Fundamentally, rehabilitation techniques ought to be examined more thoroughly in order that an agreed and standardised programme may be established post ACL repair. The current variability in rehabilitation protocols following repair or reconstruction of the injured ACL render comparison of the two surgical techniques meaningless. Without a standardised rehabilitation protocol it will not be possible to compare outcomes following ACL repair with outcomes following current ACL reconstruction.

This study demonstrates that there is no compelling evidence to support any of the rehabilitation protocols undertaken. If an accelerated protocol is to be undertaken, which may be appropriate post ACL repair but not reconstruction, then a comparison between this and standard rehabilitation needs to be supported by evidence.

5. Conclusion

No information is available from randomised trials to indicate which rehabilitation protocols may be of value for patients who have undergone primary repair of ACL rupture.

Many aspects of post-ACL reconstruction have been investigated with high level research. However, no such research has been undertaken for patients who have undergone ACL repair. No randomised control trials directly compare rehabilitation protocols following ACL repair. If such a study were not possible, then patients should be entered into a validated rehabilitation protocol following either ACL repair or reconstruction enabling a direct comparison of the surgical techniques without confounding rehabilitation differences.

It should further be added that modifications of existing rehabilitation protocols may be required for those patients who sustain multi-ligament injuries of the knee, including concomitant meniscal injury for example. These patients may require additional repair surgery, and subsequent protection of that repair which may impact significantly on the rehabilitation protocol they should follow post-operatively for their repaired ACL.

Methodologically rigorous trials are required to investigate appropriate and valid rehabilitation for these patients. Bracing type and duration, home-based rehabilitation, strengthening exercises, dietary supplementation and neuromuscular training could all impact significantly on patients following ACL repair beyond that studied among ACL reconstruction patients given the purported proprioceptive and biomechanical differences between repaired and reconstructed ACL-injured knees.

Statement of institutional review board or ethics committee approval of the study protocol

Not applicable.

Prospero registration number

CRD42020173450.

Author contributions

GH wrote the draft and conducted review of articles for inclusion.

HK reviewed and edited the draft and conducted review of articles for inclusion.

SM edited the draft, reviewed and approved the final manuscript.

Data sharing

There are no data in this manuscript.

Funding/grant support

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Financial disclosure

Declaration of competing of interestcoi, appendix 1. . search strategy.

Search strategy: " (((repair).ti,ab AND (rehabilitation).ti,ab) AND ((acl).ti,ab OR (anterior cruciate ligament).ti,ab)) AND ((random∗ trial).ti,ab OR (clinical trial).ti,ab)".

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• Review Article
• Published: 03 March 2015

Tendon injury: from biology to tendon repair

• Geoffroy Nourissat 1 ,
• Francis Berenbaum 2 &
• Delphine Duprez 3  

Nature Reviews Rheumatology volume  11 ,  pages 223–233 ( 2015 ) Cite this article

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• Developmental biology
• Miscellaneous rheumatic diseases

Tendon is a mechanosensitive tissue

Abnormal loading leads to tendon injuries

Mechanical forces are converted to biochemical signals that elicit cellular responses by tendon cells

Similar mechanical and biological signals are involved in tendon development, homeostasis and repair

A better understanding of the interaction between forces, intracellular pathways and gene transcription in the context of tendon biology is needed

Understanding mechanobiology in tendon development, homeostasis and repair is critical to designing therapies for tendon injury

Tendon is a crucial component of the musculoskeletal system. Tendons connect muscle to bone and transmit forces to produce motion. Chronic and acute tendon injuries are very common and result in considerable pain and disability. The management of tendon injuries remains a challenge for clinicians. Effective treatments for tendon injuries are lacking because the understanding of tendon biology lags behind that of the other components of the musculoskeletal system. Animal and cellular models have been developed to study tendon-cell differentiation and tendon repair following injury. These studies have highlighted specific growth factors and transcription factors involved in tenogenesis during developmental and repair processes. Mechanical factors also seem to be essential for tendon development, homeostasis and repair. Mechanical signals are transduced via molecular signalling pathways that trigger adaptive responses in the tendon. Understanding the links between the mechanical and biological parameters involved in tendon development, homeostasis and repair is prerequisite for the identification of effective treatments for chronic and acute tendon injuries.

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Acknowledgements

The authors thank S. Gournet for assistance with illustrations. The authors' work is supported by funding from the National Institute of Health and Medical Research (INSERM). D.D. also receives support from the Fondation pour la Recherche Médicale (FRM), Agence national de la recherche (ANR), Association Française contre les Myopathies, Centre national de la recherche scientifique (CNRS) and Pierre & Marie Curie University (UPMC), Fondation Arthritis Courtin and Société Française de Rhumatologie.

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Nourissat, G., Berenbaum, F. & Duprez, D. Tendon injury: from biology to tendon repair. Nat Rev Rheumatol 11 , 223–233 (2015). https://doi.org/10.1038/nrrheum.2015.26

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