Miracle-dz/UniFAR-FTUs huggingface dataset:
Short-lived plasma blasts are the main B cell effector subset during the course of multiple sclerosis

Multiple sclerosis is a chronic inflammatory and demyelinating disorder of the CNS with an unknown aetiology. Although intrathecal immunoglobulin G (IgG) synthesis is a key feature of the disease, little is still known about the B cell response in the CNS of multiple sclerosis patients. We analysed the phenotype and kinetics of different B cell subsets in patients with multiple sclerosis, infectious disease (IND) and non-inflammatory neurological disease (NIND). B cells were detected in the CSF of multiple sclerosis and IND patients, but were largely absent in NIND patients. In the CSF, the majority of B cells had a phenotype of memory B cells and short-lived plasma blasts (PB); plasma cells were absent from the compartment. The proportion of PB was highest in multiple sclerosis patients and patients with acute CNS infection. While PB disappeared rapidly from the CSF after resolution of infection in IND patients, these cells were present at high numbers throughout the disease course in multiple sclerosis patients. CSF PB numbers in multiple sclerosis patients strongly correlated with intrathecal IgG synthesis and inflammatory parenchymal disease activity as disclosed by MRI. This study identifies short-lived plasma blasts as the main effector B cell population involved in ongoing active inflammation in multiple sclerosis patients.
Pointer Analysis

Pointer analysis is a fundamental static program analysis, with a rich literature and wide applications. The goal of pointer analysis is to compute an approximation of the set of program objects that a pointer variable or expression can refer to. We present an introduction and survey of pointer analysis techniques, with an emphasis on distilling the essence of common analysis algorithms. To this end, we focus on a declarative presentation of a common core of pointer analyses: algorithms are modeled as configurable, yet easy-to-follow, logical specifications. The specifications serve as a starting point for a broader discussion of the literature, as independent threads spun from the declarative model.
SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction

Motivation Protein structure provides insight into how proteins interact with one another as well as their functions in living organisms. Protein backbone torsion angles (ϕ and ψ) prediction is a key sub-problem in predicting protein structures. However, reliable determination of backbone torsion angles using conventional experimental methods is slow and expensive. Therefore, considerable effort is being put into developing computational methods for predicting backbone angles. Results We present SAINT-Angle, a highly accurate method for predicting protein backbone torsion angles using a self-attention based deep learning network called SAINT, which was previously developed for the protein secondary structure prediction. We extended and improved the existing SAINT architecture as well as used transfer learning to predict backbone angles. We compared the performance of SAINT-Angle with the state-of-the-art methods through an extensive evaluation study on a collection of benchmark datasets, namely, TEST2016, TEST2018, CAMEO, and CASP. The experimental results suggest that our proposed self-attention based network, together with transfer learning, has achieved notable improvements over the best alternate methods. Availability and implementation SAINT-Angle is freely available as an open-source project at https://github.com/bayzidlab/SAINT-Angle. Contact shams_bayzid@cse.buet. ac.bd Supplementary information Supplementary material SM.pdf.
Modeling and Verifying Security Protocols with the Applied Pi Calculus and ProVerif

ProVerif is an automatic symbolic protocol verifier. It supports a wide range of cryptographic primitives, defined by rewrite rules or by equations. It can prove various security properties: secrecy, authentication, and process equivalences, for an unbounded message space and an unbounded number of sessions. It takes as input a description of the protocol to verify in a dialect of the applied pi calculus, an extension of the pi calculus with cryptography. It automatically translates this protocol description into Horn clauses and determines whether the desired security properties hold by resolution on these clauses. This survey presents an overview of the research on ProVerif.
Methods for Location Privacy: A comparative overview

The growing popularity of location-based services, allowing to collect huge amounts of information regarding users' location, has started raising serious privacy concerns. In this report we analyze the various kind of privacy breaches that may arise in connection with the use of location-based services, and we survey and compare the metrics and the mechanisms that have been proposed in the literature.
Complex Interactions of Darunavir in Patients with HIV and Multiple Comorbidities: Understanding Toxicity in Two Cases with Very DifferentOutcomes

Complex patients with multiple comorbidities are rarely included in large randomized studies. As a result, little is known about the optimal management of these cases. The following two cases occurred within a six month period in 2013 and were seen at Casey House, a community-based facility specializing in HIV/AIDS in Toronto, Canada. Both cases involved a serious assault to the liver believed to be drug induced liver injury (DILI) caused by darunavir. In the first case, Patient A, a 50 year-old male with a CD4 count of 454 cells/mm3 presented with tense ascites, jaundice and pedal edema. He had recently started a new anti-retroviral combination including darunavir. The ARV medications were stopped, liver function improved and his ascites was reduced with paracentesis and infusions of albumin. Chronic hepatitis B was identified. The patient was started on a new anti-retroviral regimen effective for hepatitis B. His liver failure resolved and he continues to live well in the community. In Patient B, a 49 year-old woman with CD4 count of 20 cells/mm3 and Mycobacterium Avium Complex (MAC) and hepatitis C was started on a darunavir-based regimen. She developed abdominal pain, jaundice, elevated liver function tests and anemia. HIV medications were held, and then restarted. Her symptoms worsened. Eventually all medications were stopped. Although the patient’s liver began to recover, her CD4 count remained very low and the patient developed pneumocystis pneumonia (PJP) and died. These cases are presented with a view to better understanding darunavir and its potential toxicity. The literature concerning darunavir toxicity in the setting of complex comorbidity will be reviewed.
Remembering a friend, mentor, and scholar: Dr A Norman Cranin.

T his issue of JOI is dedicated to our prestigious past Editor Dr A Norman Cranin who passed from this life at age 83 on February 20, 2011. His immediate family will miss Norman, but his ‘‘Dental Implantology family’’ will miss him also. Dr Cranin guided JOI for 38 years, and for this we can be grateful. Norman’s list of accomplishments is multiple and includes his work as a worldrenowned oral surgeon, teacher, lecturer, author, and founder of The Dr Samuel Cranin Dental Center at The Brookdale Hospital Medical Center. Norman was a true pioneer and because of his ingenuity and tireless work in implant dentistry the profession was transformed from anecdotal to science based. He was a Fellow of the Pierre Fauchard Academy, which honors the great figures of the dental profession throughout the world. Additionally, he was a Fellow of the American Academy of Implant Dentistry (AAID) and was a Diplomate and founding member of the American Board of Oral Implantology/Implant Dentistry. These words only cover a small portion of his professional accomplishments. Norman was more than a list of accomplishments. He was a friend and mentor to so many of us involved in Implant Dentistry today. There are multiple stories of his ingenuity, and his ‘‘let’s get it done’’ attitude. No implant case or project was ever too much for this Doctor. His credentials qualified him to tackle the most difficult cases with great vigor, knowledge, and skill. Many of his residents and students from Brookdale Hospital and the AAID MaxiCourse programs have gone on to help patients throughout the world. Because of this, his contributions to the profession will live on well past February 20, 2011. Norman’s work and teaching were not only felt here in the US; he was a strong supporter of the Nigerian Osseointegration and Dental Implantology Society and lectured around the globe. Personally, Norman was not only one of my mentors in dental implant surgery, but my teacher and confidant for this journal. I will always remember the support, advice, and encouragement he provided during our transition from his Editorship to mine. Norman was a master of the English language and with each visit or phone conversation, he always taught me a new word and broadened my provincial vocabulary. Norman and his wife Marilyn were always a delight to be with. The conversations were enlightening and there was much joy and laughter. Norman and Marilyn worked hard, and now the Dental Implant profession salutes their life together. May Marilyn enjoy cherished memories and Norman, good rest. EDITORIAL
A work-efficient parallel breadth-first search algorithm (or how to cope with the nondeterminism of reducers)

We have developed a multithreaded implementation of breadth-first search (BFS) of a sparse graph using the Cilk++ extensions to C++. Our PBFS program on a single processor runs as quickly as a standar. C++ breadth-first search implementation. PBFS achieves high work-efficiency by using a novel implementation of a multiset data structure, called a "bag," in place of the FIFO queue usually employed in serial breadth-first search algorithms. For a variety of benchmark input graphs whose diameters are significantly smaller than the number of vertices -- a condition met by many real-world graphs -- PBFS demonstrates good speedup with the number of processing cores. Since PBFS employs a nonconstant-time "reducer" -- "hyperobject" feature of Cilk++ -- the work inherent in a PBFS execution depends nondeterministically on how the underlying work-stealing scheduler load-balances the computation. We provide a general method for analyzing nondeterministic programs that use reducers. PBFS also is nondeterministic in that it contains benign races which affect its performance but not its correctness. Fixing these races with mutual-exclusion locks slows down PBFS empirically, but it makes the algorithm amenable to analysis. In particular, we show that for a graph G=(V,E) with diameter D and bounded out-degree, this data-race-free version of PBFS algorithm runs it time O((V+E)/P + Dlg3(V/D)) on P processors, which means that it attains near-perfect linear speedup if P << (V+E)/Dlg3(V/D).
Diagnostic Evaluation of Nontraumatic Chest Pain in Athletes

This article is a clinically relevant review of the existing medical literature relating to the assessment and diagnostic evaluation for athletes complaining of nontraumatic chest pain. The literature was searched using the following databases for the years 1975 forward: Cochrane Database of Systematic Reviews; CINAHL; PubMed (MEDLINE); and SportDiscus. The general search used the keywords chest pain and athletes. The search was revised to include subject headings and subheadings, including chest pain and prevalence and athletes. Cross-referencing published articles from the databases searched discovered additional articles. No dissertations, theses, or meeting proceedings were reviewed. The authors discuss the scope of this complex problem and the diagnostic dilemma chest pain in athletes can provide. Next, the authors delve into the vast differential and attempt to simplify this process for the sports medicine physician by dividing potential etiologies into cardiac and noncardiac conditions. Life-threatening causes of chest pain in athletes may be cardiac or noncardiac in origin, which highlights the need for the sports medicine physician to consider pathology in multiple organ systems simultaneously. This article emphasizes the importance of ruling out immediately life threatening diagnoses, while acknowledging the most common causes of noncardiac chest pain in young athletes are benign. The authors propose a practical algorithm the sports medicine physician can use as a guide for the assessment and diagnostic work-up of the athlete with chest pain designed to help the physician arrive at the correct diagnosis in a clinically efficient and cost-effective manner.
Comment évaluer une sténose carotide

La strategie therapeutique face a une stenose de la carotide interne repose en grande partie sur la determination du degre de retrecissement. Longtemps consideree comme le gold standard, l’arteriographie est de plus en plus remplacee par les methodes d’imagerie non invasives. Au premier rang de ces methodes, l’echo-Doppler constitue une technique unique permettant de recueillir en meme temps des informations morphologiques et fonctionnelles. Les criteres definissant le degre de stenose par les ultrasons sont aujourd’hui bien valides. Force est de constater cependant une heterogeneite des resultats obtenus entre les differents centres. Parmi les limites figurent en particulier les differents modes d’expression du degre de stenose et la methode de reference. L’harmonisation des resultats constitue donc un pas essentiel pour la consolidation de la methode.
Inverse vaccination with islet autoantigens to halt progression of autoimmune diabetes

The incidence of autoimmune diabetes mellitus is growing worldwide; currently the only treatment is injection of insulin formulations to maintain glycemic control. Islet transplantation has been examined as a potential cure for diabetes. However, it has several limitations, including side effects of immunosuppressive agents required to prevent graft rejection. Other approaches have been to examine immune modulation to halt or prevent the autoimmune attack, with the hope that by preventing tissue damage, it will eventually regenerate and permit patients to be free from insulin injections. The focus of the current review is the three major antigen‐based vaccines, insulin, glutamic acid decarboxylase 65 (GAD65; Diamyd), and heat shock protein 60 (Hsp60; DiaPep277), with respect to their mechanism of action, preclinical results, and published results from clinical trials. Despite promising results with these three antigens in mice and humans, efficacy has been limited in clinical trials. Drug Dev Res 72:788–804, 2011. © 2011 Wiley Periodicals, Inc.
Flashes and floaters

Patients commonly present to GPs because they have seen flashing lights in their visual fields. These symptoms can reflect long-standing degenerative processes or can be caused by acute sight- threatening eye disease or occasionally neurological disease. ‘Floaters’ are seen as dots or spots that ‘float’ in front of everything looked at by the person. They may occur alone or in association with flashes. This article aims to provide GPs with a strategy to separate those patients with flashes and/or floaters who simply require reassurance, from those who require referral to eye casualty or for neurological assessment.
Dietary habits prone to lifestyle-related disease

Objective: To evaluate relations among dietary habits, bone mineral density (BMD), visceral fat area (VFA), and arterial stiffness and recommend better dietary habits. Methods: One hundred and six men and 381 women (aged 18–84) received a health checkup and answered questionnaires, with subsequent measurements of BMD (speed of sound), VFA (bioelectrical impedance), and arterial stiffness (acceleration plethysmography). Results: Snacking, intake of meat, fried foods, sweet foods, and instant foods were associated with higher BMD; regular lunch hours, skipping meals, calorie restriction, and eating moderate amounts were associated with lower BMD as indicated using analysis of variance (ANOVA) analysis. Only skipping meals was an independent factor of high BMD. Age was an independent factor of low BMD, large VFA, and high arterial stiffness. Female sex was an independent factor of low BMD and VFA as indicated using multiple regression analysis. Conclusions and implications: BMD was associated with eating behaviours and food contents, among which only skipping meals was an independent contributor.
Iron Supplementation for Female Athletes: Effects on Iron Status and Performance Outcomes

Iron is an essential micronutrient involved in oxidative metabolism and critical to exercise performance. The prevalence of iron deficiency (ID) is much higher in active women for a variety of reasons, and poor iron status has been shown to be detrimental to overall health as well as physical performance. Iron status can be assessed using a number of indicators; however clinical cut-offs for active populations remain controversial. Randomized, placebo-controlled supplementation trials of iron-depleted female athletes have shown that oral iron supplementation in doses of 100-mg FeSO4·d−1 (approximately 20 mg elemental iron) improves iron status and may improve measures of physical performance. It is recommended that female athletes most at risk of ID be screened at the beginning of and during the training season using hemoglobin and serum ferritin, and appropriate dietary and/or supplementation recommendations be made to those with compromised iron status.
Prediction of energy expenditure and physical activity in preschoolers.

PURPOSE Accurate, nonintrusive, and feasible methods are needed to predict energy expenditure (EE) and physical activity (PA) levels in preschoolers. Herein, we validated cross-sectional time series (CSTS) and multivariate adaptive regression splines (MARS) models based on accelerometry and heart rate (HR) for the prediction of EE using room calorimetry and doubly labeled water (DLW) and established accelerometry cut points for PA levels. METHODS Fifty preschoolers, mean ± SD age of 4.5 ± 0.8 yr, participated in room calorimetry for minute-by-minute measurements of EE, accelerometer counts (AC) (Actiheart and ActiGraph GT3X+), and HR (Actiheart). Free-living 105 children, ages 4.6 ± 0.9 yr, completed the 7-d DLW procedure while wearing the devices. AC cut points for PA levels were established using smoothing splines and receiver operating characteristic curves. RESULTS On the basis of calorimetry, mean percent errors for EE were -2.9% ± 10.8% and -1.1% ± 7.4% for CSTS models and -1.9% ± 9.6% and 1.3% ± 8.1% for MARS models using the Actiheart and ActiGraph+HR devices, respectively. On the basis of DLW, mean percent errors were -0.5% ± 9.7% and 4.1% ± 8.5% for CSTS models and 3.2% ± 10.1% and 7.5% ± 10.0% for MARS models using the Actiheart and ActiGraph+HR devices, respectively. Applying activity EE thresholds, final accelerometer cut points were determined: 41, 449, and 1297 cpm for Actiheart x-axis; 820, 3908, and 6112 cpm for ActiGraph vector magnitude; and 240, 2120, and 4450 cpm for ActiGraph x-axis for sedentary/light, light/moderate, and moderate/vigorous PA (MVPA), respectively. On the basis of confusion matrices, correctly classified rates were 81%-83% for sedentary PA, 58%-64% for light PA, and 62%-73% for MVPA. CONCLUSIONS The lack of bias and acceptable limits of agreement affirms the validity of the CSTS and MARS models for the prediction of EE in preschool-aged children. Accelerometer cut points are satisfactory for the classification of sedentary, light, and moderate/vigorous levels of PA in preschoolers.
Total Mandibular Reconstruction and Rehabilitation: A Case Report.

T reatment of mandibular discontinuity defects is a great clinical challenge. Partial or complete mandibulectomy is the surgical treatment of choice for patients diagnosed with malignant oral lesions involving the mandible. The use of microvascular grafts to minimize the impairment of function, speech, and esthetics is the mainstay of modern surgical approach of the reconstructive team. Advances in microvascular surgery have provided the surgeon with methods to repair the partially resected mandible with vital bone grafts. Vascularized bone is used for the secondary reconstructions with large defect, where soft tissue is inadequate, or where the recipient bed has been compromised by radiation, chronic infection, or previous surgery. Often, however, reconstruction of the bony defect alone does not guarantee an adequate foundation for successful conventional prosthetic rehabilitation. Osseointegrated implants placed into the microvascularized grafted bone offer an opportunity for improved function and patient satisfaction and have become the preferred treatment modality. A variety of donor sites have been used for this purpose, including the iliac crest, radius, scapula, and fibula. However, currently the microvascular free fibula flap represents a versatile reconstruction method after mandibularablation. The free fibular microvascular flap was one of the earliest osseous free flaps with successful application in large bony defects. Hidalgo was the first to report the use of a fibula vascularized flap for mandibular reconstruction with 100% osseous survival in a series of 13 patients. Some of the documented advantages of using free fibular microvascular flaps are
Effect of controlled breathing on short-term cardiovascular variability: An investigation in chronic heart failure patients

Voluntary control of breathing (CB) has been proposed as a means to standardize short-term investigations on cardiovascular variability (CVV). In this study, we assessed the changes induced by CB on ventilatory and cardiovascular parameters in 17 chronic heart failure (CHF) patients. We recorded the instantaneous lung volume (ILV), R-R interval (RR), systolic arterial pressure (SAP) and end-tidal CO/sub 2/ (ETCO/sub 2/, 10 patients only) during 8 minutes of spontaneous breathing (SB) and 8 minutes of CB at 0.22 Hz. CB caused a 14% reduction in respiratory rate, a 57% increase in tidal volume, a 27% increase in minute ventilation and a 7% decrease in ETCO/sub 2/. A negligible change was observed in mean RR and SAP. No significant change was observed in the low-frequency (LF) power of RR and SAP and in baroreflex sensitivity, whereas the high-frequency (HF) power increased markedly. Hence, CB in CHF patients causes a mild hyperventilation but does not seem to influence autonomic cardiovascular control. Only respiratory-related oscillations of CVV signals are affected by CB.