Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanistic Insight into the Reactivation of BCAII Enzyme from Denatured and Molten Globule States by Eukaryotic Ribosomes and Domain V rRNAs

In all life forms, decoding of messenger-RNA into polypeptide chain is accomplished by the ribosome. Several protein chaperones are known to bind at the exit of ribosomal tunnel to ensure proper folding of the nascent chain by inhibiting their premature folding in the densely crowded environment of the cell. However, accumulating evidence suggests that ribosome may play a chaperone role in protein folding events in vitro. Ribosome-mediated folding of denatured proteins by prokaryotic ribosomes has been studied extensively. The RNA-assisted chaperone activity of the prokaryotic ribosome has been attributed to the domain V, a span of 23S rRNA at the intersubunit side of the large subunit encompassing the Peptidyl Transferase Centre. Evidently, this functional property of ribosome is unrelated to the nascent chain protein folding at the exit of the ribosomal tunnel. Here, we seek to scrutinize whether this unique function is conserved in a primitive kinetoplastid group of eukaryotic species Leishmania donovani where the ribosome structure possesses distinct additional features and appears markedly different compared to other higher eukaryotic ribosomes. Bovine Carbonic Anhydrase II (BCAII) enzyme was considered as the model protein. Our results manifest that domain V of the large subunit rRNA of Leishmania ribosomes preserves chaperone activity suggesting that ribosome-mediated protein folding is, indeed, a conserved phenomenon. Further, we aimed to investigate the mechanism underpinning the ribosome-assisted protein reactivation process. Interestingly, the surface plasmon resonance binding analyses exhibit that rRNA guides productive folding by directly interacting with molten globule-like states of the protein. In contrast, native protein shows no notable affinity to the rRNA. Thus, our study not only confirms conserved, RNA-mediated chaperoning role of ribosome but also provides crucial insight into the mechanism of the process.
A paradigmatic object-oriented programming language: Design, static typing and semantics

Abstract To illuminate the fundamental concepts involved in object-oriented programming languages, we describe the design of TOOPL, a paradigmatic, statically-typed, functional, object-oriented programming language which supports classes, objects, methods, hidden instance variables, subtypes and inheritance. It has proven to be quite difficult to design such a language which has a secure type system. A particular problem with statically type checking object-oriented languages is designing typechecking rules which ensure that methods provided in a superclass will continue to be type correct when inherited in a subclass. The type-checking rules for TOOPL have this feature, enabling library suppliers to provide only the interfaces of classes with actual executable code, while still allowing users to safely create subclasses. To achieve greater expressibility while retaining type-safety, we choose to separate the inheritance and subtyping hierarchy in the language. The design of TOOPL has been guided by an analysis of the semantics of the language, which is given in terms of a model of the F-bounded second-order lambda calculus with fixed points at both the element and type level. This semantics supports the language design by providing a means to prove that the type-checking rules are sound, thus guaranteeing that the language is type-safe. While the semantics of our language is rather complex, involving fixed points at both the element and type level, we believe that this reflects the inherent complexity of the basic features of object-oriented programming languages. Particularly complex features include the implicit recursion inherent in the use of the keyword, self, to refer to the current object, and its corresponding type, MyType. The notions of subclass and inheritance introduce the greatest semantic complexities, whereas the notion of subtype is more straightforward to deal with. Our semantic investigations lead us to recommend caution in the use of inheritance, since small changes to method definitions in subclasses can result in major changes to the meanings of the other methods of the class.
Severity and clustering of menopausal symptoms among obese and nonobese postmenopausal women in India

Background: The symptoms of menopause have a negative impact on quality of life, especially in women transitioning to menopause and earlier transitions. This study was conducted with the objective of assessing the effect of obesity on the severity of menopausal symptoms and the clustering of symptoms in postmenopausal women in India. Methodology: The Menopausal Rating Scale (MRS) was used to assess the severity of menopausal symptoms of postmenopausal women of Chennai, visiting Saveetha Medical College, Chennai, India. This cross-sectional study was conducted from August to November 2013 in Chennai, India. Sociodemographic characteristics, anthropometric measurements, blood pressure level, menopausal history, personal health history, and hormonal disorder issues were investigated. Results: The results have shown that 24% of the participants had complaint of mild to severe hot flushes, half of them had reported heart ailments (49%; n = 74), and disturbed sleep (48%; n = 72). The proportion of overweight/obese participants was higher in married (64%) than widows (41%), and this difference was found statistically significant (P = 0.005). There were no significant differences in MRS scores of obese and nonobese postmenopausal participants. Conclusion: There is a need of developing interactive, user friendly, technology based education module for addressing the chronic ailments of postmenopausal women.
Identification of Barrett's Esophagus in Relatives by Endoscopic Screening

AIM:Familial aggregation of Barrett's esophagus and its associated cancers has been termed familial Barrett's esophagus (FBE). The aim of the study was to determine whether endoscopic screening would identify Barrett's esophagus (BE) in relatives of probands with BE or esophageal adenocarcinoma (EAC). METHODS:All living first-degree relatives of patients with long segment BE or EAC presenting to the endoscopy suite of two academic hospitals were sent validated questionnaires inquiring about gastroesophageal reflux symptoms and prior endoscopic evaluation. First-degree relatives of affected probands or affected relatives who reported no prior upper endoscopy were offered screening unsedated esophagoscopy. Relatives with chronic gastroesophageal reflux symptoms were also offered an alternative of conventional sedated upper endoscopy. The yield of screening endoscopy was measured. Screening endoscopy findings were then compared between family members of known FBE patients and those with “isolated” disease.RESULTS:One hundred and ninety-eight relatives from 69 families, 23 known FBE probands and 46 probands with apparently “isolated” disease, were enrolled. Forty relatives (29 FBE relatives and 11 relatives of probands with “isolated” disease) reported prior upper endoscopy. Screening upper endoscopies performed on 62 (25 FBE and 37 “isolated” disease relatives) of the remaining 158 relatives identified Barrett's epithelium in 13 (21%). Compared to probands with apparently “isolated” disease, Barrett's epithelium (EAC, BE, or SSBE) was identified significantly more often in siblings and offspring of FBE probands, p≤ 0.05. Endoscopic screening of relatives of FBE probands identified a multigeneration multiplex FBE pedigree consistent with an autosomally dominant inherited trait. Endoscopic screening of relatives of probands with reported “isolated” diseased did not identify any new FBE pedigrees.CONCLUSIONS:Endoscopy identified EAC, long-segment BE, and short-segment BE in a substantial proportion of first-degree relatives of affected members of FBE families. A familial susceptibility to develop Barrett's epithelium appears to be present in a subset of patients with BE and EAC.
From antisocial behavior to violence: a model for the amplifying role of coercive joining in adolescent friendships.

BACKGROUND Aggression is one of the more stable characteristics of child and adolescent development, and violent behavior in early adulthood is often foreshadowed by aggressive behavior in childhood and early adolescence. Considerable evidence has linked coercive family interactions to aggressive behavior in childhood, but less research has been conducted on the joint role of family and peer interaction in the escalation of aggression to violence in adulthood. METHODS We coded family interactions at age 12-13 and friendship interaction at age 16-17 in a multiethnic sample of youth and families. Violence in young adulthood (age 22-23) was measured using self-report, criminal records, and parent report. We tested the hypothesis that a process of 'coercive joining' in friendship interactions mediated the relationship between coercive family interactions and serious violence. RESULTS We found that observed coercive joining in friendships at age 16-17 predicted early-adulthood violent behavior over and above an established tendency toward antisocial behavior. We also found that observed coercive family interactions at age 12 predicted early-adulthood violence, and that coercive joining with friends fully mediated this link. CONCLUSIONS These results significantly extend coercion theory by suggesting that coercive joining in the context of peer groups is an additional mechanism by which coercive processes in the family are extended and amplified to violent behavior in early adulthood. Our findings suggest the importance of addressing both individual interpersonal skills and self-organizing peer groups when intervening to prevent violent behavior.
Transplantation in the patient with hepatitis C

Hepatitis C virus (HCV) infection is the most frequent cause of liver disease after renal transplantation. Its clinical course is irrelevant in the short term, except for rare cases of fibrosing cholestatic hepatitis. However, in the long run, HCV infection can lead to major liver complications. Because interferon (IFN) is generally contraindicated in renal transplant patients, the best approach is to treat patients on dialysis. Until more information with pegylated‐IFN is available, the use of alpha‐IFN monotherapy is recommended. Most of the patients with sustained virological response remain HCV RNA negative after transplantation. HCV‐positive renal transplant patients have a higher risk for proteinuria, chronic rejection, infections and post‐transplant diabetes (PTDM). Long‐term patient‐ and graft‐survival rates are lower in HCV‐positive patients. Mortality is higher, mainly as a result of liver disease and infections. HCV can contribute to the development of certain neoplasias such as post‐transplant lymphoproliferative disease (PTLD). HCV infection is also an independent risk factor for graft loss. PTDM, transplant glomerulopathy and HCV‐related glomerulonephritis can contribute to graft failure. Despite this, transplantation is the best option for end‐stage renal disease in HCV‐positive patients. Several measures to minimize the consequences of HCV infection have been recommended. Adjustment of immunosuppression and careful follow up in the outpatient clinic for early detection of HCV‐related complications are mandatory.
Matching pursuits video coding: Dictionaries and fast implementation

Matching pursuits over a basis of separable Gabor functions has been demonstrated to outperform DCT methods for displaced frame difference coding for video compression. Unfortunately, apart from very low bit-rate applications, the algorithm involves an extremely high computational load. This paper contains an original contribution to the issues of dictionary selection and fast implementation for matching pursuits video coding. First, it is shown that the PSNR performance of existing matching pursuits codecs can be improved and the implementation cost reduced by a better selection of dictionary functions. Secondly, dictionary factorization is put forward to further reduce implementation costs. A reduction of the computational load by a factor of 20 is achieved compared to implementations reported to date. For a majority of test conditions, this reduction is supplemented by an improvement in reconstruction quality. Finally, a pruned full-search algorithm is introduced, which offers significant quality gains compared to the better-known heuristic fast-search algorithm, while keeping the computational cost low.
Learning to Act Properly: Predicting and Explaining Affordances from Images

We address the problem of affordance reasoning in diverse scenes that appear in the real world. Affordances relate the agent's actions to their effects when taken on the surrounding objects. In our work, we take the egocentric view of the scene, and aim to reason about action-object affordances that respect both the physical world as well as the social norms imposed by the society. We also aim to teach artificial agents why some actions should not be taken in certain situations, and what would likely happen if these actions would be taken. We collect a new dataset that builds upon ADE20k [32], referred to as ADE-Affordance, which contains annotations enabling such rich visual reasoning. We propose a model that exploits Graph Neural Networks to propagate contextual information from the scene in order to perform detailed affordance reasoning about each object. Our model is showcased through various ablation studies, pointing to successes and challenges in this complex task.
The Challenge of Big Data in Public Health: An Opportunity for Visual Analytics

Public health (PH) data can generally be characterized as big data. The efficient and effective use of this data determines the extent to which PH stakeholders can sufficiently address societal health concerns as they engage in a variety of work activities. As stakeholders interact with data, they engage in various cognitive activities such as analytical reasoning, decision-making, interpreting, and problem solving. Performing these activities with big data is a challenge for the unaided mind as stakeholders encounter obstacles relating to the data’s volume, variety, velocity, and veracity. Such being the case, computer-based information tools are needed to support PH stakeholders. Unfortunately, while existing computational tools are beneficial in addressing certain work activities, they fall short in supporting cognitive activities that involve working with large, heterogeneous, and complex bodies of data. This paper presents visual analytics (VA) tools, a nascent category of computational tools that integrate data analytics with interactive visualizations, to facilitate the performance of cognitive activities involving big data. Historically, PH has lagged behind other sectors in embracing new computational technology. In this paper, we discuss the role that VA tools can play in addressing the challenges presented by big data. In doing so, we demonstrate the potential benefit of incorporating VA tools into PH practice, in addition to highlighting the need for further systematic and focused research.
Color Invariants for Person Reidentification

We revisit the problem of specific object recognition using color distributions. In some applications-such as specific person identification-it is highly likely that the color distributions will be multimodal and hence contain a special structure. Although the color distribution changes under different lighting conditions, some aspects of its structure turn out to be invariants. We refer to this structure as an intradistribution structure, and show that it is invariant under a wide range of imaging conditions while being discriminative enough to be practical. Our signature uses shape context descriptors to represent the intradistribution structure. Assuming the widely used diagonal model, we validate that our signature is invariant under certain illumination changes. Experimentally, we use color information as the only cue to obtain good recognition performance on publicly available databases covering both indoor and outdoor conditions. Combining our approach with the complementary covariance descriptor, we demonstrate results exceeding the state-of-the-art performance on the challenging VIPeR and CAVIAR4REID databases.
Adapting Crossover in Evolutionary Algorithms

One of the issues in evolutionary algorithms (EAs) is the relative importance of two search operators: mutation and crossover. Genetic algorithms (GAs) and genetic programming (GP) stress the role of crossover, while evolutionary programming (EP) and evolution strategies (ESs) stress the role of mutation. The existence of many different forms of crossover further complicates the issue. Despite theoretical analysis, it appears difficult to decide a priori which form of crossover to use, or even if crossover should be used at all. One possible solution to this difficulty is to have the EA be self-adaptive, i.e., to have the EA dynamically modify which forms of crossover to use and how often to use them, as it solves a problem. This paper describes an adaptive mechanism for controlling the use of crossover in an EA and explores the behavior of this mechanism in a number of different situations. An improvement to the adaptive mechanism is then presented. Surprisingly this improvement can also be used to enhance performance in a non-adaptive EA.
Detecting psychiatric disorders in medical practice using the General Health Questionnaire. Why do cut-off scores vary?

Synopsis In this study we assessed the accuracy of the General Health Questionnaire in detecting psychiatric disorders in general medical out-patients. A total of 290 newly referred patients were interviewed with the Present State Examination. Prior to the interview, 112 patients completed the full GHQ-60, 100 completed the GHQ-30 and 78 completed the GHQ-12. Data from the first group were used to study the full GHQ-60, together with the GHQ-30 and and GHQ-12, when disembedded from the full questionnaire. In a comparison between the disembedded and the separate versions of the GHQ-30 and GHQ-12 we observed considerable variation in the cut-off scores where a certain sensitivity and specificity was attained. In ROC-analysis, the versions were not materially different in their discriminatory capacity (area under the curve). The use of different criteria to define a ‘case’ demonstrated that case severity was another source of increasing cut-off scores. Our data demonstrate that the use of disembedded or separate versions of the questionnaire, together with variation in the case criteria can be a major explanation for variation in cut-off scores that was observed in previous studies.
Substitution of standard soybean oil with olive oil-based lipid emulsion in parenteral nutrition: comparison of vascular, metabolic, and inflammatory effects.

CONTEXT Soybean oil-based lipid emulsions are the only Food and Drug Administration-approved lipid formulation for clinical use in parenteral nutrition (PN). Recently concerns with its use have been raised due to the proinflammatory effects that may lead to increased complications because they are rich in ω-6 polyunsaturated fatty acids. METHODS This was a prospective, randomized, controlled, crossover study comparing the vascular, metabolic, immune, and inflammatory effects of 24-h infusion of PN containing soybean oil-based lipid emulsion (Intralipid), olive oil-based (ClinOleic), lipid free, and normal saline in 12 healthy subjects. RESULTS Soybean oil-PN increased systolic blood pressure compared with olive oil-PN (P < 0.05). Soybean oil PN reduced brachial artery flow-mediated dilatation from baseline (-23% at 4 h and -25% at 24 h, both P < 0.01); in contrast, olive oil PN, lipid free PN, and saline did not change either systolic blood pressure or flow-mediated dilatation. Compared with saline, soybean oil PN, olive oil PN, and lipid free PN similarly increased glucose and insulin concentrations during infusion (P < 0.05). There were no significant changes in plasma free fatty acids, lipid profile, inflammatory and oxidative stress markers, immune function parameters, or sympathetic activity between soybean oil- and olive oil-based lipid emulsions. CONCLUSION The 24-h infusion of PN containing soybean oil-based lipid emulsion increased blood pressure and impaired endothelial function compared with PN containing olive oil-based lipid emulsion and lipid-free PN in healthy subjects. These vascular changes may have significant implications in worsening outcome in subjects receiving nutrition support. Randomized controlled trials with relevant clinical outcome measures are needed in patients receiving PN with olive oil-based and soybean oil-based lipid emulsions.
Multi-scale modeling of plasticity and damage of lath martensite in multi-phase steels

Lath martensite is an important phase in a number of high strength steels. It shows a hierarchical microstructure in which the morphology is intrinsically related to the crystallography. A summary of the main experimental evidence of interlath retained austenite films in low carbon, low alloyed martensite is given in this chapter. Existing micro-mechanical investigations show that lath martensite deforms plastically, preferentially along the lath habit plane. It is therefore argued that the presence of thin austenite films at lath boundaries might trigger the observed deformation behaviour at the micro-scale. In this chapter, a brief survey is given of the historical developments of the research on the subject. Some main achievements are emphasized, which will serve the next chapters in setting up a modelling framework capable to predict the main features of the mechanical behaviour of lath martensite. Therefore, this survey does not aim for completeness.
Andes Virus Antigens Are Shed in Urine of Patients with Acute Hantavirus Cardiopulmonary Syndrome

ABSTRACT Hantavirus cardiopulmonary syndrome (HCPS) is a highly pathogenic emerging disease (40% case fatality rate) caused by New World hantaviruses. Hantavirus infections are transmitted to humans mainly by inhalation of virus-contaminated aerosol particles of rodent excreta and secretions. At present, there are no antiviral drugs or immunotherapeutic agents available for the treatment of hantaviral infection, and the survival rates for infected patients hinge largely on early virus recognition and hospital admission and aggressive pulmonary and hemodynamic support. In this study, we show that Andes virus (ANDV) interacts with human apolipoprotein H (ApoH) and that ApoH-coated magnetic beads or ApoH-coated enzyme-linked immunosorbent assay plates can be used to capture and concentrate the virus from complex biological mixtures, such as serum and urine, allowing it to be detected by both immunological and molecular approaches. In addition, we report that ANDV-antigens and infectious virus are shed in urine of HCPS patients.