Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants for Neoantigen Identification

All tumors accumulate genetic alterations, some of which can give rise to mutated, non-self peptides presented by human leukocyte antigen (HLA) molecules and elicit T-cell responses. These immunogenic mutated peptides, or neoantigens, are foreign in nature and display exquisite tumor specificity. The correlative evidence suggesting they play an important role in the effectiveness of various cancer immunotherapies has triggered the development of vaccines and adoptive T-cell therapies targeting them. However, the systematic identification of personalized neoantigens in cancer patients, a critical requisite for the success of these therapies, remains challenging. A growing amount of evidence supports that only a small fraction of all tumor somatic non-synonymous mutations (NSM) identified represent bona fide neoantigens; mutated peptides that are processed, presented on the cell surface HLA molecules of cancer cells and are capable of triggering immune responses in patients. Here, we provide an overview of the existing strategies to identify candidate neoantigens and to evaluate their immunogenicity, two factors that impact on neoantigen identification. We will focus on their strengths and limitations to allow readers to rationally select and apply the most suitable method for their specific laboratory setting.
Iron deficiency anemia among preschool children belonging to affluent families in Kerala, India

Context: Anemia leads to impaired cognitive function, growth, and psychomotor development. Zeroing in on a specific socioeconomic or demographic group and a specific type of anemia, may help in better planning of resources in our battle against anemia. Aims: The aim of this study is to determine the prevalence, severity, risk factors (age, gender, and nutrition status) of iron deficiency anemia (IDA) in apparently healthy preschool children (6–59 months) belonging to affluent families. Settings and Design: A cross-sectional study conducted in a private teaching hospital. Subjects and Methods: A total of 160 children aged 6–59 months, belonging to the upper middle class, who came to the pediatric outpatient department for routine visits over a period of 1 year were evaluated. Sociodemographic data with hemoglobin, red cell indices and iron studies of blood samples were estimated. Statistical Analysis Used: Continuous data were described as mean and standard deviation. Odds ratio with 95% confidence interval was calculated using multiple logistics regression. Results: Among the 160 children evaluated, 48 (30%) were anemic, of which 41 (85.4%) had IDA. Equal proportion (P = 0.84) of boys (25.0%) and girls (26.4%) and equal proportion (P = 0.75) of well-nourished (26.2%) and moderately nourished (23.3%) had IDA. A higher proportion (P < 0.0001) of children below the age of two (40.7%) had IDA. Children below the age of 2 years were more likely to have IDA (Odds ratio [OR]: 5.8 95% confidence interval [CI] 2.5–13.8) irrespective of gender and nutrition. Conclusions: A high prevalence among apparently healthy children from affluent families is an indicator that the general population rates will be even higher. This study highlights the need to plan further intervention trials with either iron-rich or iron-fortified foods or iron supplementation, especially among children below the age of 2.
Dexmeditomedine as an adjuvant reduces the minimum effective anesthetic volume of ropivacaine required for supraclavicular brachial plexus nerve block

Background: Dexmeditomidine has been used as an adjuvant with local anaesthetic amides for supraclavicular brachial plexus block for improving the quality and duration of analgesia. We conducted this study to find out that whether as an adjuvant it reduces the minimum effective anaesthetic concentration (MEAC) and minimum effective anaesthetic volume (MEAV). Materials and Methods: 90 patients undergoing upper limb surgery were randomized into three groups and given ultrasound guided supraclavicular block. Group A received 30 ml of 0.5% Ropivacaine, Group B received 20 ml of 0.5% ropivacaine with 50μgm dexmeditomidine and Group C received 15 ml of 0.5% ropivacaine with 50μgm of dexmeditomidine. The onset of sensory and motor block, the duration of sensory and motor block, quality of analgesia, haemodynamic and sedative parameters were recorded. SPSS software was used for statistical analysis. Results: The onset of sensory block in Group B(9.47±3.54mins) and Group C (12.45±3.86) was faster in comparison to Group A(17.64±5.36) which was statistically significant. The duration of the block was also more in Group B and C in comparison to Group A. The requirement of rescue analgesia was also less in Group B and C. There were no statistically significant changes in the haemodynamic parameters and sedation scores. Although the patients of Group C received lesser volume and dose of ropivacaine than Group B, there was no statistically significant delay in onset or duration of sensory and motor block neither any change in the quality of analgesia. Conclusion: We concluded that 15 ml of ropivacaine with 50μgm of dexmeditomidine is adequate for good quality of analgesia with no compromise on onset of analgesia and duration of block.
An in vivo double-blind randomized controlled study comparing the postoperative pain in single sitting root canal treatment under bupivacaine versus lignocaine used as a local anesthetic agent

Aim: This in vivo double-blind randomized control trial was carried out to evaluate the efficacy of a long-acting local anesthetic bupivacaine in preventing postoperative pain associated with single sitting endodontic treatment and to compare it with lignocaine when used as a local anesthetic agent. Methods: A total of fifty patients with symptomatic irreversible pulpitis were selected to be included in the study. The patients were randomly divided into two groups: Group A patients were given lignocaine as local anesthetic and Group B were given bupivacaine. The root canal procedures for the patients were carried out in single sittings under rubber dam using hand ProTaper™ system, 2.5% sodium hypochlorite as irrigant alternating with normal saline and obturation by lateral condensation technique. A questionnaire employing visual analog scale for pain assessment was given to the patient and instructions on how to fill the form were given. The patients were recalled after 2 days, and the pain was analyzed. The result was tabulated and statistically analyzed for incidence and degree of pain. Results: The mean overall postoperative pain for bupivacaine was lesser than that for lignocaine, and the difference was statistically significant. Conclusion: Based on our findings and in comparison with those of other studies, we reached the conclusion that it may be recommended that bupivacaine may replace lignocaine as the anesthetic of choice in the single visit endodontic protocol in order to reduce the incidence of postoperative pain often seen after single visit endodontic procedures.
Dimensional correlation between morphology and root canal anatomy in mesiobuccal root of permanent maxillary first molar: An ex vivo study

Aim: The aim of the present study was to establish a correlation between morphology and root canal anatomy of mesiobuccal (MB) root of the permanent maxillary first molar using cone-beam computed tomography (CBCT) and stereomicroscope. Methodology: Access cavities were prepared on sixty permanent maxillary first molars. Efforts were made to locate MB second (MB2) canals without magnification and with magnification using methylene blue dye and ultrasonic troughing. The number of teeth possessing MB2 canal with both methods was recorded. Thereafter, the MB root was resected and observed under CBCT. The MB root was then sectioned at different levels and observed under stereomicroscope. Both the methods were used to assess the number of canals and root forms which were classified as long oval, oval, and round. The data thus obtained were then subjected to statistical analysis using ANOVA and Z-test. Results: Clinical techniques such as magnification, dyes, and troughing were found to be more efficient in the detection of MB2 canals as compared to unaided techniques. As observed with CBCT and stereomicroscope, the incidence of MB2 canal was significantly more in coronal as compared to middle and apical, and a statistical correlation between root form and number of canals was observed. Conclusion: Majority of the MB roots were long oval and oval in axial section and the incidence of finding MB2 in long oval and oval root forms was found to be greater as compared to round root form, although it is not necessary that all long oval or oval roots shall have two or more canals.
Prevalence of nicotine dependence and its impact on quality of life and severity of symptoms in schizophrenic patients

Aims and Objectives: The aim of the study is (1) To assess the prevalence of nicotine dependence and its impact on quality of life and severity of symptoms in patients with schizophrenia. (2) To determine the association between ND and clinical symptomatology of schizophrenia. (3) To explore the impact of ND on the quality of life (QOL) of patients with schizophrenia. Materials and Methods: The current study is a cross-sectional study done among 100-male schizophrenic patients conducted in the Department of Psychiatry, Mamata General Hospital, Khammam, Telangana, from July 2017 to December 2017. The tools used are the Fagerstrom test for ND (FTND) was administered to assess ND. The Positive and Negative Syndrome Scale (PANSS) for assessing the clinical symptomatology, and the abbreviated World Health Organization QOL (WHOQOL-BREF) for assessing their QOL. Results: The prevalence of smoking in schizophrenics was 68.75%. Prevalence of ND is higher in illiterates, unemployment, nuclear family, low-socioeconomic status, and hailing from the rural background when compared to that of the nicotine nondependence. Nicotine-dependent were found to be having higher mean scores on the positive subscale and the General Psychopathology Subscale and lower mean scores on negative domain. Within the ND group, correlation testing between the FTND scores and PANSS revealed a negative co-relationship between ND and negative symptoms, whereas the correlation testing between the FTND scores and WHOQOL-BREF scores revealed a negative relationship between ND and psychological, social, and environment domains of QOL. There was a negative correlation between (a) Negative symptoms and all the domain of QOL. (b) General psychopathology and social relationships, environmental among ND. Summary and Conclusion: Nicotine-dependent patients suffer from the higher levels of symptoms and enjoy a worse QOL compared to that of the nondependent patients with schizophrenia. Bearing in mind the innumerable harms of ND, the evaluation and management of ND must become an integral aspect of the evaluation and management of patients with schizophrenia.
Spinal anaesthesia in paediatric orthopaedic services: A five year experience in a Nigeria hospital

Background: The role of spinal anesthesia (SA) as a primary anesthetic technique in children is not a common practice in many centers in Nigeria. The reason for the poor utilization might be due to lack of expertise in pediatric SA, fear of adverse effect such as spinal cord injury. Objectives: This study is a retrospective audit of the anesthetic technique in the pediatric age group in a private orthopedic hospital in Nigerian. The outcome of this study will help reduce the misconception regarding its practicability and safety. Materials and Methods: This is a 5-year single center retrospective study of the anesthetic choice for surgeries on the lower limb in the pediatric age group in an orthopedic hospital. The survey extended from 2012 to 2016 and all relevant information obtained from the medical records of the surgical theatres of the hospital as well as anesthetic records of the patients. The children were assigned to four groups: I – neonates; II – infants 1 month–2 years; III – children 2–12 years; and IV – 12–16 years. Results: A total of 156 patients' records were reviewed. Spinal-induced hypotension occurred only in 4 patients (2.56%). All the 4/44 patients (9.09%) who had hypotension were in the adolescent age group. Conclusion: This study showed the feasibility of SA and good safety profile in the pediatric age group.
Accuracy of magnetic resonance imaging of the shoulder in evaluation of anterior shoulder instability

Background: Shoulder arthroscopy is currently considered the gold standard in diagnosing shoulder pathologies. Although magnetic resonance imaging (MRI) has an established accuracy in determining labral injuries following glenohumeral instability, the opinions of surgeons and radiologists regarding MRIs are still inconsistent till date. The aim of this study was to carry out a diagnostic evaluation of MRI vis-a-vis shoulder arthroscopy for the assessment of Bankart and Hill-Sachs lesions in subjects of anterior shoulder instability. Subjects and Methods: This was a diagnostic evaluation study, estimating the accuracy of MRI in diagnosing lesions encountered in shoulder dislocations vis-a-vis shoulder arthroscopy. Ninety participants of anterior shoulder dislocation were evaluated preoperatively with a shoulder MRI. The study participants were later subjected to a diagnostic shoulder arthroscopy and managed operatively on a case-to-case basis. Results: The sensitivity and specificity of MRI to diagnose a Bankart lesion were 90.78% and 85%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) were 97% and 63% for the same. The sensitivity and specificity of MRI to diagnose a Hill–Sachs lesion were 92.68% and 85.71%, respectively. The PPV and NPV were 84.44% and 93.33% for the same. The diagnostic accuracy for MRI detection of Bankart lesion was 91% and of Hill–Sachs lesion was 88.89%. Conclusions: MRI is a very sensitive and specific tool in the detection of lesions commonly associated with shoulder instability, namely Bankart and Hill–Sachs lesions.
Efficacy of smear layer removal by two Ayurvedic herbal irrigants, using continuous vs. syringe and needle irrigation

Introduction: A successful root canal therapy is largely dependent on thorough chemo-mechanical debridement of the root canal space. However, mechanical preparation inadvertently forms an amorphous layer, known as the “smear layer. ” Traditionally used irrigants have a deleterious effect over root dentin and thus herbal alternatives can be a better option for smear layer removal with no action on root dentin. Aim: The purpose of the study was to compare the in vitro effectiveness of two potential herbal irrigants: 6% German chamomile extract (GCE) and 6% Morinda citrifolia juice (MCJ), in removal of smear layer. Materials and Methods: Eighty single-rooted human teeth were allocated into two equal groups: one to be instrumented with the self-adjusting file (SAF), while the other with WaveOne (WO). Four subgroups in each group were irrigated with 6% GCE, 6% MCJ, 17% ethylenediaminetetraacetic acid (EDTA) (positive control), and NS (negative control). Scanning electron microscopy (SEM) was used to evaluate the presence of smear layer. Statistical Analysis: As data for smear layer were categorical, Chi-square test was applied for data analysis. P < 0.05 was considered statistically significant. Results: The most effective smear layer removal in the coronal part was observed with SAF-EDTA and SAF-GCE, followed by WO-EDTA. In the middle part, SAF-GCE was equivalent to that of SAF-EDTA, followed by WO-EDTA and WO-GCE. In the apical third, the most efficient smear layer removal was observed with SAF-EDTA, followed by some removal of smear layer by WO-EDTA and SAF-GCE. GCE was as effective as EDTA in removal of smear layer in the coronal and mid-root regions, when used with continuous irrigation.
Surveillance of microorganisms associated with dental caries patients attending at a Tertiary Care Indian Teaching Hospital

Backgrounds: Dental caries patients are developed day by day in all age groups and predominantly in children. It is caused due to microorganisms mainly. Here, we find the organisms associated with dental caries of patients attending at Institute of Dental Science, Bhubaneswar, India. Materials and Methods: This prospective study was carried out from February to May 2018 at Institute of Dental Science, Bhubaneswar, India. A total number of 135 samples were collected from dental caries patients and processed in different agar media for identification of organisms, and the percentage of antibiotic susceptibility was evaluated. Results: Out of 135 patient samples, 112 organisms were isolated and identified with both culture and biochemical tests. Among all, 9 Enterococcus sp. (6.66%), 27 coagulase-negative Staphylococcus aureus sp. (20%), 6 Bacillus sp. (4.44%), and 30 Streptococcus sp. (22.22%) were found as Gram-positive cocci; 3 Acinetobacter sp. (2.22%), 6 Pseudomonas sp. (4.44%), 21 Shigella sp. (15.55%), and 6 Citrobacter freundii sp. (4.44%) were identified as Gram-negative bacteria; and 6 Candida glabrata (4.44%), 3 Candida albicans (2.22%), and 3 Candida tropicalis (2.22%) were identified as budding yeast colonies. In antibiotic resistance patterns, it was revealed that penicillin is the most resistance (92%) and gentamycin is the most sensitive antibiotic (79.2%) for bacteria associated with dental caries. Conclusion: Dental caries caused due to microbial infection is cured with antibiotics. Out of all antibiotics, gentamicin is more sensitive and preferable for dental caries with this study. Hence, a clinician can prescribe gentamicin beside amoxicillin and cefixime for early treatments.
MSys: uma ferramenta de acompanhamento de atividades para sistemas de aprendizado eletrônico.

E-learning content creation is not an easy task, but its evaluation is even more complex. In order to evaluate if the content is adequate to the students needs, it would be helpful to know how the student assimilated the learning content, how he reacted to it and the period of time spent on the learning object. Besides, considering the different cognitive features of learning and the possibility of adjustment of the didactic content, it could help teacher’s evaluation in an available online course. This work describes a monitoring system (Msys) that tracks the level of utilization of student’s activities, and presents summarized and comparative results to the teacher and the student. Even though the widespread use of several LMS (Learning Management System) environments today, the importance of tools capable of offering a detailed monitoring of student’s activities has not been recognized. This work focus on how the tool was created using current standards on digital content construction, defining functional requirements to its development and presenting simulation results that is a proof-ofconcept. Also, it is presented a prototype of the tool, validating the interfaces of capture and results presentation, showing that is possible to integrate it to online learning systems, bringing benefits to the teacher evaluation.
Automated Software Vulnerability Assessment with Concept Drift

Software Engineering researchers are increasingly using Natural Language Processing (NLP) techniques to automate Software Vulnerabilities (SVs) assessment using the descriptions in public repositories. However, the existing NLP-based approaches suffer from concept drift. This problem is caused by a lack of proper treatment of new (out-of-vocabulary) terms for the evaluation of unseen SVs over time. To perform automated SVs assessment with concept drift using SVs' descriptions, we propose a systematic approach that combines both character and word features. The proposed approach is used to predict seven Vulnerability Characteristics (VCs). The optimal model of each VC is selected using our customized time-based cross-validation method from a list of eight NLP representations and six well-known Machine Learning models. We have used the proposed approach to conduct large-scale experiments on more than 100,000 SVs in the National Vulnerability Database (NVD). The results show that our approach can effectively tackle the concept drift issue of the SVs' descriptions reported from 2000 to 2018 in NVD even without retraining the model. In addition, our approach performs competitively compared to the existing word-only method. We also investigate how to build compact concept-drift-aware models with much fewer features and give some recommendations on the choice of classifiers and NLP representations for SVs assessment.
Simple Mechanisms for Profit Maximization in Multi-item Auctions

We study a classical Bayesian mechanism design problem where a seller is selling multiple items to a buyer. We consider the case where the seller has costs to produce the items, and these costs are private information to the seller. How can the seller design a mechanism to maximize her profit? Two well-studied problems, revenue maximization in multi-item auctions and signaling in ad auctions, are special cases of our problem. We show that there exists a simple mechanism whose profit is at least 1/11 the optimal profit, when the buyer has a constraint-additive valuation over independent items. The approximation factor becomes 6 when the buyer is additive. Our result holds even when the seller's costs are correlated across items. We introduce a new class of mechanisms called permit-selling mechanisms. These mechanisms have two stages. For each item i, we create a separate permit that allows the buyer to purchase the item at its cost. In the first stage, we sell the permits without revealing any information about the costs. In the second stage, the seller reveals all the costs, and the buyer can buy item i by only paying the cost $c_i$ if the buyer has purchased the permit for item i in the first stage. We show that the best permit-selling mechanism or the best posted price mechanism is already a constant factor approximation to the optimal profit (6 for additive, and 11 for constrained additive). Indeed, we do not require the optimal permit-selling mechanism, only selling the permits separately or as a grand bundle suffices to achieve the above approximation ratio. Our proof is enabled by constructing a benchmark for the optimal profit via a novel dual solution and a new connection to revenue maximization in multi-item auctions with a subadditive bidder.
Dependency Versioning in the Wild

Many modern software systems are built on top of existing packages (modules, components, libraries). The increasing number and complexity of dependencies has given rise to automated dependency management where package managers resolve symbolic dependencies against a central repository. When declaring dependencies, developers face various choices, such as whether or not to declare a fixed version or a range of versions. The former results in runtime behaviour that is easier to predict, whilst the latter enables flexibility in resolution that can, for example, prevent different versions of the same package being included and facilitates the automated deployment of bug fixes. We study the choices developers make across 17 different package managers, investigating over 70 million dependencies. This is complemented by a survey of 170 developers. We find that many package managers support — and the respective community adapts — flexible versioning practices. This does not always work: developers struggle to find the sweet spot between the predictability of fixed version dependencies, and the agility of flexible ones, and depending on their experience, adjust practices. We see some uptake of semantic versioning in some package managers, supported by tools. However, there is no evidence that projects switch to semantic versioning on a large scale. The results of this study can guide further research into better practices for automated dependency management, and aid the adaptation of semantic versioning.