Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.
Prediction of Yarn Paths in Braided Structures Formed on a Square Pyramid

A circular braiding process is used for producing three-dimensional (3D) textile preforms using 3D mandrels. In our previous study, we have predicted and simulated the yarns paths on various 3D mandrels, including cylinder, square prism, and cones with circular and elliptical cross-sections (Rawal, A., Potluri, P. and Steele, C. (2005). Geometrical Modeling of the Yarn Paths in Three-Dimensional Branded Structure, Journal of Industrial Textiles, 34(2): 115–135. ). This study predicts the yarn paths on a square pyramid in which the yarns are modeled as straight lines varying in length from the top to the bottom of the square pyramid. The 3D coordinates of the yarn paths on a square pyramid have been mathematically related to the braid angle.
3D Shape Modelling through a Constrained Estimation of a Bicubic B-spline Surface

This paper presents a new method to extract the 3D shape of objects from 3D gray level images using a bicubic B-spline surface model. Extraction of object shape is achieved through a hierarchical surface fitting by exploiting the multi-scale representation of the model. A strategy for converting the surface estimation into curve estimations is devised. The model surface is estimated by successively computing a set of cubic B-spline curves consisting of a coordinate curve net defining the surface. A regularising component is incorporated into the curve estimation to encourage the generation of an orthogonal coordinate curve net, preventing the creation of unwanted creases. Experimental results are presented for extracting the 3D shape of objects from real 3D images.
Restricted expression of Fgf16 within the developing chick inner ear

Fibroblast growth factor (FGF) signaling is required for otic placode induction and patterning of the developing inner ear. We have cloned the chick ortholog of Fgf16 and analyzed its expression pattern in the early chick embryo. Expression is restricted to the otic placode and developing inner ear through all the stages examined. By the closed otocyst stage, expression has resolved to anterior and posterior domains that partially overlap with those of bone morphogenetic protein 4 (Bmp4), a marker of the developing sensory patches, the cristae of the anterior and posterior semicircular canals. Platelet‐derived growth factor alpha (PDGFA), another growth factor with restricted otic expression, also overlaps with Fgf16 expression. The restricted expression pattern of Fgf16 suggests a role for FGF signaling in the patterning of the sensory cristae, together with BMP signaling. Developmental Dynamics 235:2276–2281, 2006. © 2006 Wiley‐Liss, Inc.
Psychosocial profile of HIV-infected adolescents in a Southern US urban cohort

Abstract We undertook a retrospective medical chart review of HIV-infected adolescents referred to a Southern US urban comprehensive adolescent HIV clinic between 1992 and 2003 to describe the psychosocial profile of adolescents infected with HIV via high-risk behaviours. Ninety-one adolescents (59 females, 32 males, 95% African-American, median age 17 years) were identified. Common reasons for initial HIV testing included routine prenatal screening (20%), clinical symptoms suggestive of HIV (20%), and recognized risk-related behaviours (20%). Findings included a history of unstable housing in the previous year (27%), running away (29%), knowing someone with HIV (36%), parental substance abuse (reported by youth, 46%), parental abandonment/neglect (30%), high substance use rates (marijuana 33%, tobacco 27%), current/prior STDs (60%), and involvement with the juvenile justice system or incarceration (41%). Sexual abuse/assault was reported by 41%. Previous depression was reported in 15% with approximately half reporting prior hospitalization. An additional 12% of the cohort had current clinical depressive symptoms. We conclude that infections with HIV via high-risk behaviours during adolescence occur in youth with multiple psychosocial stressors. Targeted prevention efforts to reduce these underlying stressors may decrease new adolescent infection. HIV-infected youth are best served in a comprehensive care environment with immediate access to medical care, social work, and psychology/psychiatry services.
Automatic Bug Triage using Semi-Supervised Text Classification

Abstract —In this paper, we propose a semi-supervised text classification approach for bug triage to avoid the deficiency of labeled bug reports in existing supervised approaches. This new approach combines naive Bayes classifier and expectation-maximization to take advantage of both labeled and unlabeled bug reports. This approach trains a classifier with a fraction of labeled bug reports. Then the approach iteratively labels numerous unlabeled bug reports and trains a new classifier with labels of all the bug reports. We also employ a weighted recommendation list to boost the performance by imposing the weights of multiple developers in training the classifier. Experimental results on bug reports of Eclipse show that our new approach outperforms existing supervised approaches in terms of classification accuracy. Keywords- automatic bug triage; expectation-maximization; semi-supervised text classification; weighted recommendation list I. I NTRODUCTION Most of large software projects employ a bug tracking system (bug repository) to manage bugs and developers. In software development and maintenance, a bug repository is a significant software repository for storing the bugs submitted by
Investigating Testing Approaches for Dynamically Adaptive Systems Work in Progress

Software systems that can automatically adapt to changes in their environments – also know as Dynamically Adaptive Systems (DAS) – play increasingly important roles in society’s everyday life. The growing demand for such systems, which range from simple mobile interactive gaming applications to complex crisis management systems, requires specific development methodologies that encompass the full software life cycle. The EU-funded DiVA project (Dynamic Variability in Complex, Adaptive Systems) [1] aims at providing a toolsupported methodology for developing DASs. The DiVA framework addresses the management of dynamic variability through a combination of aspect-oriented and model-driven techniques. Within the DiVA project context, we are interested in developing testing strategies that can adequately handle the issues involved in testing DASs. In particular, the combinatorial explosion of variant composition alternatives, many of which probably unforeseen at design time, and the runtime nature of system re-configuration, makes testing a daunting task for software developers. We started our investigation by performing a systematic mapping study of testing approaches for DASs. The goals of our survey were two: (RQ1) identifying the challenges authors have described so far in the context of DASs testing; and (RQ2) identifying candidate testing approaches which can be customised to address the challenges within the scope of the DiVA project. In regard to the research question (RQ1), we enumerated the following challenges:
Comparison of Novel and Known Neuroprotectants for Treating Exposure to Different Types of Toxins

Abstract : Studies using cultured brain slices have found that compensatory signals are activated in response to different types of excitotoxicity/seizures related to environmental toxin or military threat agent exposure. Soman, an irreversible anticholinesterase and devastating weapon of mass destruction, produces convulsions, memory impairment, and cell loss in the brain, especially in the hippocampus. Soman-induced accumulation of acetylcholine initiates mechanisms responsible for the development of incapacitating seizures. However, another excitatory neurotransmitter, glutamate, also has been linked to the toxic action of the chemical agent We found that after repeated exposures to sub-toxic levels of soman, long-term hippocampal slice cultures from rat exhibit enhanced vulnerability to brief excitotoxic episodes of glutamate receptor over-stimulation. In particular, the hippocampal tissue became sensitive to cytoskeletal damage and synaptic decline in response to secondary pathogenic events. Thus, seemingly innocuous soman exposures leave the brain vulnerable to excitotoxic insults that are implicated in traumatic brain injury and stroke. The findings also suggest that asymptomatic exposures to soman can lead to hippocampal damage and that early indicators of low-level soman contact are critical for the prevention of subsequent brain injury. Studies with receptor modulators are helping to identify key signal transduction pathways that lead to neuroprotection vs. those that enhance neuronal vulnerability. Accordingly, a neuroprotectant that acts against excitotoxicity through the MAP kinase pathway eliminates soman-induced neuronal vulnerability.
Congenital Stapes Anomalies with Normal Eardrum

Objectives A non-progressive and conductive hearing loss with normal eardrum, but no history of trauma and infection, is highly suggestive of a congenital ossicular malformation. Among ossicular anomalies, stapes anomaly is the most common. The purpose of this study is to describe patterns of stapes anomaly and to analyze its surgical outcome with special reference to its patterns. Methods We conducted a retrospective case review. The subjects comprised 66 patients (76 ears) who were decisively confirmed by the exploratory tympanotomy as congenital stapes anomalies without any anomalies of the tympanic membrane and external auditory canal. The preoperative and postoperative audiological findings, temporal bone computed tomography scan, and operative findings were analyzed. Results There were 16 anomalous patterns of stapes among which footplate fixation was the most common anomaly. These 16 patterns were classified into 4 types according to the status of stapes footplate. Successful hearing gain was achieved in 51 out of 76 ears (67.1%) after surgical treatment. Conclusion Footplate fixation was usually bilateral, whereas stapes anomalies associated with other ossicular anomaly were usually unilateral. The success of the surgical treatment of stapes anomaly might depend on its developmental status of the footplate. Stapes anomalies were detected without any fixed patterns, therefore, it is quite possible to detect a large variety of patterns in future.
The p63 gene in EEC and other syndromes

Several autosomal dominantly inherited human syndromes have recently been shown to result from mutations in the p63 gene. These syndromes have various combinations of limb malformations fitting the split hand-split foot spectrum, orofacial clefting, and ectodermal dysplasia. The p63 syndrome family includes the EEC syndrome, AEC syndrome, ADULT syndrome, limb-mammary syndrome, and non-syndromic split hand/foot malformation. The pattern of heterozygous mutations is distinct for each of these syndromes. The functional effects on the p63 proteins also vary between syndromes. In all of these syndromes, the mutation appears to have both dominant negative and gain of function effects rather than causing a simple loss of function.
c-kitpos GATA-4 High Rat Cardiac Stem Cells Foster Adult Cardiomyocyte Survival through IGF-1 Paracrine Signalling

Background Resident c-kit positive (c-kitpos) cardiac stem cells (CSCs) could be considered the most appropriate cell type for myocardial regeneration therapies. However, much is still unknown regarding their biological properties and potential. Methodology/Principal Findings We produced clones of high and low expressing GATA-4 CSCs from long-term bulk-cultured c-kitpos CSCs isolated from adult rat hearts. When c-kitpos GATA-4 high expressing clonal CSCs (cCSCs) were co-cultured with adult rat ventricular cardiomyocytes, we observed increased survival and contractility of the cardiomyocytes, compared to cardiomyocytes cultured alone, co-cultured with fibroblasts or c-kitpos GATA-4 low expressing cCSCs. When analysed by ELISA, the concentration of IGF-1 was significantly increased in the c-kitpos GATA-4 high cCSC/cardiomyocyte co-cultures and there was a significant correlation between IGF-1 concentration and cardiomyocyte survival. We showed the activation of the IGF-1 receptor and its downstream molecular targets in cardiomyocytes co-cultured with c-kitpos GATA-4 high cCSCs but not in cardiomyocytes that were cultured alone, co-cultured with fibroblasts or c-kitpos GATA-4 low cCSCs. Addition of a blocking antibody specific to the IGF-1 receptor inhibited the survival of cardiomyocytes and prevented the activation of its signalling in cardiomyocytes in the c-kitpos GATA-4 high cCSC/cardiomyocyte co-culture system. IGF-1 supplementation or IGF-1 high conditioned medium taken from the co-culture of c-kitpos GATA-4 high cCSCs plus cardiomyocytes did extend the survival and contractility of cardiomyocytes cultured alone and cardiomyocytes co-cultured with c-kitpos GATA-4 low cCSCs. Conclusion/Significance c-kitpos GATA-4 high cCSCs exert a paracrine survival effect on cardiomyocytes through induction of the IGF-1R and signalling pathway.
Learning causality for news events prediction

The problem we tackle in this work is, given a present news event, to generate a plausible future event that can be caused by the given event. We present a new methodology for modeling and predicting such future news events using machine learning and data mining techniques. Our Pundit algorithm generalizes examples of causality pairs to infer a causality predictor. To obtain precise labeled causality examples, we mine 150 years of news articles, and apply semantic natural language modeling techniques to titles containing certain predefined causality patterns. For generalization, the model uses a vast amount of world knowledge ontologies mined from LinkedData, containing ~200 datasets with approximately 20 billion relations. Empirical evaluation on real news articles shows that our Pundit algorithm reaches a human-level performance.
Prognostic indicators of adverse renal outcome and death in acute kidney injury hospital survivors

Introduction: Data regarding prognostic factors of post-discharge mortality and adverse renal function outcome in acute kidney injury (AKI) hospital survivors are scarce and controversial. Objectives: We aimed to identify predictors of post-discharge mortality and adverse renal function outcome in AKI hospital survivors. Patients and Methods: The study group consisted of 84 AKI hospital survivors admitted to the tertiary medical center during 2-year period. Baseline clinical parameters, with renal outcome 3 months after discharge and 6-month mortality were evaluated. According survival and renal function outcome, patients were divided into two groups. Results: Patients who did not recover renal function were statistically significantly older (P < 0.007) with higher Charlson comorbidity index (CCI) score (P < 0.000) and more likely to have anuria and oliguria (P = 0.008) compared to those with recovery. Deceased AKI patients were statistically significantly older (P < 0.000), with higher CCI score (P < 0.000), greater prevalence of sepsis (P =0.004), higher levels of C-reactive protein (CRP) (P < 0.017) and ferritin (P < 0.051) and lower concentrations of albumin (P<0.01) compared to survivors. By multivariate analysis, independent predictors of adverse renal outcome were female gender (P =0.033), increasing CCI (P =0.000), presence of pre-existing chronic kidney disease (P =0.000) and diabetes mellitus (P =0.019) as well as acute decompensated heart failure (ADHF) (P =0.032), while protective factor for renal function outcome was higher urine output (P =0.009). Independent predictors of post-discharge mortality were female gender (P =0.04), higher CCI score (P =0.001) and sepsis (P =0.034). Conclusion: Female AKI hospital survivors with increasing burden of comorbidities, diagnosis of sepsis and ADHF seem to be at high-risk for poor post-discharge outcome.
Prevention of chemotherapy-induced nausea and vomiting: focus on fosaprepitant

Fosaprepitant is a prodrug of aprepitant, a neurokinin1 (NK1) receptor antagonist used in prophylactic antiemetic regimens used prior to cytotoxic chemotherapy. Fosaprepitant is being developed to provide a parenterally administered alternative to the orally administered aprepitant. Fosaprepitant is rapidly converted to aprepitant and an intravenous dose of 115 mg is bioequivalent to 125 mg orally, with similar plasma concentrations at 24 hours. In phase I and II trials fosaprepitant shows efficacy, but the large randomized efficacy studies have utilized aprepitant. When it is added to dexamethasone and a 5HT3 receptor antagonist on day 1 prior to chemotherapy aprepitant improves the control of acute post chemotherapy emesis and when continued on days 2 and 3 with dexamethasone it demonstrated even greater improvement in the control of delayed emesis. This has been shown with both cisplatin-containing regimens and those based upon cyclophosphamide and an anthracycline. Fosaprepitant is well tolerated with mild to moderate venous irritation being the only additional toxicity to those seen with oral aprepitant, and that is a function of dose, concentration, and infusion rate. Headaches are the other toxicity most commonly reported. Fosaprepitant can be used as a parenteral alternative to aprepitant in regimens to control chemotherapy-induced emesis.
Power Allocation for Full-Duplex Relaying-Based D2D Communication Underlaying Cellular Networks

Device-to-device (D2D) communications allow direct transmissions between two proximate user equipments (UEs), which can improve local services in cellular networks. Considering full-duplex (FD) relaying can achieve higher spectrum and energy efficiency than half-duplex (HD) relaying, we propose a new D2D communication scheme that allows D2D links to underlay cellular downlink by assigning D2D transmitters as FD relays to assist cellular downlink transmissions. The system objective is to optimize the achievable rates for the D2D users while fulfilling the minimum rate requirements of the cellular users. To this end, we first derive the achievable rates for both the D2D users and the cellular users. Then we accomplish the system target by optimizing the transmission powers at the base station (BS) and at the D2D transmitter. Under the aggregate power constraint, we can solve the optimal power-allocation problem in closed form. The simulation results show that the proposed FD relaying-based D2D communication scheme outperforms the traditional cellular communication mode and the existing HD relaying-based D2D communication scheme in the maximal achievable rate.
A Novel Autotransporter Adhesin Is Required for Efficient Colonization during Bubonic Plague

ABSTRACT Many proteins secreted by the type V secretion system (autotransporters) have been linked to virulence in gram-negative bacteria. Several putative conventional autotransporters are present in the Yersinia pestis genome, but only one, YapE, is conserved in the other pathogenic Yersinia species. Here, we introduce YapE and demonstrate that it is secreted via a type V mechanism. Inactivation of yapE in Y. pestis results in decreased efficiency in colonization of tissues during bubonic infection. Coinfection with wild-type bacteria only partially compensates for this defect. Analysis of the host immune response suggests that YapE is required for either efficient colonization at the inoculation site or dissemination to draining lymph nodes. YapE also demonstrates adhesive properties capable of mediating interactions with bacteria and eukaryotic cells. These findings support a role for YapE in modulating host-pathogen interactions that are important for colonization of the mammalian host.
Automatic Assessment of Communication Skill in Non-conventional Interview Settings: A Comparative Study

Effective communication is an important social skill that facilitates us to interpret and connect with people around us and is of utmost importance in employment based interviews. This paper presents a methodical study and automatic measurement of communication skill of candidates in different modes of behavioural interviews. It demonstrates a comparative analysis of non-conventional methods of employment interviews namely 1) Interface-based asynchronous video interviews and 2)Written interviews (including a short essay). In order to achieve this, we have collected a dataset of 100 structured interviews from participants. These interviews are evaluated independently by two human expert annotators on rubrics specific to each of the settings. We, then propose a predictive model using automatically extracted multimodal features like audio, visual and lexical, applying classical machine learning algorithms. Our best model performs with an accuracy of 75% for a binary classification task in all the three contexts. We also study the differences between the expert perception and the automatic prediction across the settings.
VODCA: View-Oriented, Distributed, Cluster-Based Approach to Parallel Computing

This paper presents a high-performance distributed shared memory system called VODCA, which supports a novel view-oriented parallel programming on cluster computers. One advantage of view-oriented parallel programming is that it allows the programmer to participate in performance optimization through wise partitioning of the shared data into views. Another advantage of this programming style is that it enables the underlying distributed shared memory system to optimize consistency maintenance. VODCA implements a view-based consistency model and uses an efficient view-oriented update protocol with Integrated Diff to maintain consistency of a view. Important implementation details of VODCA are described in this paper. Experimental results demonstrate that VODCA performs very well and its performance is comparable with MPI (message passing interface) systems
Field emission from carbon nanotubes and its application to electron sources

Field emission from (i) as-grown multiwall nanotubes (MWNTs), (ii) purified MWNTs and (iii) purified single-wall nanotubes (SWNTs) was investigated by field emission microscopy (FEM). As an application of nanotube field emitters, we manufactured cathode ray tube (CRT) lighting-elements by replacing conventional thermionic cathodes with nanotube field emitters. Stable electron emission, high emission current with low electric field (∼10 mA/cm2 at 1.5 V/μm), and long life of the emitters were demonstrated.