Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Substrate Glycoside Linkage and Elemental Sulfur on Bioenergetics of and Hydrogen Production by the Hyperthermophilic Archaeon Pyrococcus furiosus

ABSTRACT Glycoside linkage (cellobiose versus maltose) dramatically influenced bioenergetics to different extents and by different mechanisms in the hyperthermophilic archaeon Pyrococcus furiosus when it was grown in continuous culture at a dilution rate of 0.45 h−1 at 90°C. In the absence of S0, cellobiose-grown cells generated twice as much protein and had 50%-higher specific H2 generation rates than maltose-grown cultures. Addition of S0 to maltose-grown cultures boosted cell protein production fourfold and shifted gas production completely from H2 to H2S. In contrast, the presence of S0 in cellobiose-grown cells caused only a 1.3-fold increase in protein production and an incomplete shift from H2 to H2S production, with 2.5 times more H2 than H2S formed. Transcriptional response analysis revealed that many genes and operons known to be involved in α- or β-glucan uptake and processing were up-regulated in an S0-independent manner. Most differentially transcribed open reading frames (ORFs) responding to S0 in cellobiose-grown cells also responded to S0 in maltose-grown cells; these ORFs included ORFs encoding a membrane-bound oxidoreductase complex (MBX) and two hypothetical proteins (PF2025 and PF2026). However, additional genes (242 genes; 108 genes were up-regulated and 134 genes were down-regulated) were differentially transcribed when S0 was present in the medium of maltose-grown cells, indicating that there were different cellular responses to the two sugars. These results indicate that carbohydrate characteristics (e.g., glycoside linkage) have a major impact on S0 metabolism and hydrogen production in P. furiosus. Furthermore, such issues need to be considered in designing and implementing metabolic strategies for production of biofuel by fermentative anaerobes.
Renal Transplantation From Pediatric Donors in the United Kingdom

Background Significant disparity exists in the United Kingdom between the need for organ transplant and supply of deceased donor organs. In the recent years, efforts to increase donation has improved the rate of mainly deceased donors after circulatory death and from older donors. The rate of donation from pediatric population has remained low and those younger than 2 years including neonatal donation has remained largely unexplored. Methods A retrospective review of the outcome of renal transplantation from pediatric donor (<18 years) kidneys in the United Kingdom. Results Our results show a poor referral and conversion rate, and high discard rate (43%) of kidneys procured from donors younger than 2 years. During the 15-year study period (1997–2011), 47 donors younger than 2 years were referred (3 per year). Of these, 26 proceeded to donation resulting in 17 transplants (65% utilization). The referral rate for donors 2 years or older to younger than 5 years also remains low (76 in 15 years), but the conversion (88%) and utilization rates (73%) are better in this group. There was better utilization in donors aged 5 years or older to younger than 18 years. Overall graft and patient survival remains excellent in all 3 groups; with comparable survival of 82%, 85%, and 77% (P = 0.29) with mean follow-up periods of 9, 12.5, and 11.8 years, respectively. Conclusions Despite excellent outcome, the referral, donation, and utilization of kidneys from donors younger than 5 years and particularly those younger than 2 years remain low. We suggest implementing improved strategies to increase donation from this group of population.
KOWALSKI: Collecting API Clients in Easy Mode

Understanding API usage is important for upstream and downstream developers. However, compiling a dataset of API clients is often a tedious task, especially since one needs many clients to draw a representative picture of the API usage.In this paper, we present KOWALSKI, a tool that takes the name of an API, then finds and downloads client binaries by exploiting the Maven dependency management system. As a case study, we collect clients of Apache Lucene, the de facto standard for full-text search, analyze the binaries, and create a typed call graph that allows developers to identify hotspots in the API.A video demonstrating how KOWALSKI is used for this experiment can be found at https://youtu.be/zdx28GnoSRQ.
Evaluation of pain management interventions for neonatal circumcision pain.

INTRODUCTION The purpose of the study was to determine the efficacy of music and eutectic mixture of local anesthetics (EMLA) on pain responses of neonates undergoing circumcision. METHOD A randomized, double-blind experimental design was used with 23 neonates. Pain response was measured using an observational pain intensity rating scale and the physiologic parameters of heart rate, respiratory rate, oxygen saturation levels, salivary cortisol levels, and length of cry. Each infant's state was examined for a potential contribution to the pain response. FINDINGS Infant state, salivary cortisol levels, and respiratory rates were not significant. Pain ratings had considerable variability for all treatment conditions, but both single treatment groups had less pain by the end of the procedure. The heart rate was significantly lower for the EMLA group and remained stable for the music group. Oxygen saturation differences were statistically significant for the music group (P =.02) and approached significance for the EMLA group. DISCUSSION Preliminary support was provided for the efficacy of EMLA and music to contribute to the pain relief of neonates undergoing circumcision. Further study is warranted. Neonates deserve interventions that will provide them with a less painful start in life.
An Exploration of Data-Driven Hint Generation in an Open-Ended Programming Problem

Data-driven systems can provide automated feedback in the form of hints to students working in problem solving environments. Programming problems present a unique challenge to these systems, in part because of the many ways in which a single program can be written. This paper reviews current strategies for generating data-driven hints for programming problems and examines their applicability to larger, more open-ended problems, with multiple, loosely ordered goals. We use this analysis to suggest directions for future work to generate hints for these problems.
One-Class Classification-Based Real-Time Activity Error Detection in Smart Homes

Caring for individuals with dementia is frequently associated with extreme physical and emotional stress, which often leads to depression. Smart home technology and advances in machine learning techniques can provide innovative solutions to reduce caregiver burden. One key service that caregivers provide is prompting individuals with memory limitations to initiate and complete daily activities. We hypothesize that sensor technologies combined with machine learning techniques can automate the process of providing reminder-based interventions. The first step toward automated interventions is to detect when an individual faces difficulty with activities. We propose machine learning approaches based on one-class classification that learn normal activity patterns. When we apply these classifiers to activity patterns that were not seen before, the classifiers are able to detect activity errors, which represent potential prompt situations. We validate our approaches on smart home sensor data obtained from older adult participants, some of whom faced difficulties performing routine activities and thus committed errors.
Interleukin‐6 is an important mediator for mitochondrial DNA repair after alcoholic liver injury in mice

We investigated the hypothesis that a prominent effect of chronic ethanol consumption is mitochondrial DNA (mtDNA) injury and compared this injury in IL‐6 knockout (KO) and wild‐type (WT) mice. Ethanol feeding for 4 weeks resulted in steatosis and oxidative mtDNA damage (8‐OHdG) in both IL‐6KO and WT mice. However, the WT mice were able to repair the injury by increased production of mtDNA repair enzymes (OGG‐1, Neil 1) and check point (p21, p53) proteins and avoid the mtDNA mutations. By contrast the IL‐6 KO mice were unable to repair mtDNA resulting in deletions and diminished transcription of the mtDNA encoded protein cytochrome c oxidase subunit‐I (COI). The mitochondrial injury was reflected by decreased membrane potential, reduced levels of ATP, and apoptosis‐inducing factor (AIF)‐induced apoptosis. Conclusion: IL‐6 plays a critical role in allowing the liver to recover from significant mtDNA oxidation caused by alcohol. The data suggests that IL‐6 activates mtDNA repair enzymes and induces cell cycle arrest allowing time for mtDNA repair. (HEPATOLOGY 2010;)
Reliability assessment of microgrids with renewable generation by an hybrid model

This paper presents the reliability evaluation of microgrids with distributed generation based on renewable energy sources and storage systems. A hybrid model that combines the analytical approach with state sampling is used in order to consider the intermittence of renewable sources, like wind, solar and small hydro power plants. Batteries are used to reduce the supply intermittence of both the solar and wind generation. The battery state of charge is considered through a specific model. The influence of microgrids on the distribution network power supply reliability is evaluated, together with several relevant aspects, such as the islanding operation success probability, the feeder capacity for load transfer, the battery charge level and size and the type of the renewable source.
Compressed C4.5 Models for Software Defect Prediction

Defects in every software must be handled properly, and the number of defects directly reflects the quality of a software. In recent years, researchers have applied data mining and machine learning methods to predicting software defects. However, in their studies, the method in which the machine learning models are directly adopted may not be precise enough. Optimizing the machine learning models used in defects prediction will improve the prediction accuracy. In this paper, aiming at the characteristics of the metrics mined from the open source software, we proposed three new defect prediction models based on C4.5 model. The new models introduce the Spearman's rank correlation coefficient to the basis of choosing root node of the decision tree which makes the models better on defects prediction. In order to verify the effectiveness of the improved models, an experimental scheme is designed. In the experiment, we compared the prediction accuracies of the existing models and the improved models and the result showed that the improved models reduced the size of the decision tree by 49.91% on average and increased the prediction accuracy by 4.58% and 4.87% on two modules used in the experiment.
Improving Enterprise Architecture Evaluation Based on Concepts from the Normalized Systems Theory

In this paper, the authors present the results of a design science research project to develop a method for the evaluation of enterprise architecture projects. The methodology is based on the SAAM methodology, and applies concepts from the Normalized Systems theory to provide a more systematic way of performing architectural evaluations. They first discuss the problem statement, the objectives of our solution and the design of the method. The authors then demonstrate how the method has been applied in a real-life organization. Finally, they evaluate the proposed method using the criteria formulated in our problem statement.
Presynaptic Dopamine in Schizophrenia

Presynaptic dopamine (DA) transmission has been measured in schizophrenia using different paradigms aimed at providing estimates of the integrity or the activity of the presynaptic dopaminergic neuron. Researchers have measured: (1) DA synthesis capacity with [18F]DOPA, a measure of the activity of dopa decarboxylase, (2) DA release with studies measuring the impact of a DA releasing stimulant challenge on the binding of a D2 receptor radiotracer, (3) D2 baseline occupancy by DA, a measure of baseline intrasynaptic DA, assessed by the changes in binding of D2 radiotracer induced by DA depletion, and (4) the DA and the vesicular monoamine transporters, to assess the integrity of presynaptic terminals. The relationship between DA release and D2 receptor occupancy at baseline by DA has also been assessed in the same patients. Overall, these different imaging modalities have converged to show a dysregulation of presynaptic dopaminergic activity in schizophrenia, leading to excessive DA release in the striatum, particularly in the projection to the associative striatum, an area of integration between cognitive and limbic cortical inputs. Excessive striatal presynaptic DA is linked to the emergence of acute psychotic symptoms and to their response to treatment in schizophrenia. Understanding the etiology of this dysregulation and its consequences on the rest of the circuitry is important for future drug development.
DSL-maps: From requirements to design of domain-specific languages

Domain-Specific Languages (DSLs) are central to Model-Driven Engineering, where they are used for creating models for particular domains. However, current research and tools for building DSLs focus on the design and implementation aspects of the DSL, while the requirements analysis phase, and its automated transition to design is largely neglected. In order to alleviate this situation, we propose DSL-maps, a notation inspired by mind-maps, to represent requirements for DSLs. The notation is supported by a tool, which helps in the automated transition into an initial meta-model design, using a customizable transformation and recommendations from a catalogue of meta-model design patterns.
La résistivité de la gémination en tarifit.

This investigation reports on gemination in Tarifit Berber. It presents results of an acoustic investigation of singleton and geminate voiceless stops, produced in intervocalic position at a normal and fast speaking rate. They show that geminates are systematically produced with longer closure durations compared to singletons. Gemination, however, does not affect the duration of adjacent vowels, neither does it affect the duration of VOT. In addition, this contrast is shown to be resistant to increased speaking rate. Results are discussed in the light of X-ray data obtained in a previous companion study.
Opportunistic bronchopulmonary infections after lung transplantation: clinical and radiographic findings.

PURPOSE To assess clinical and radiographic findings in opportunistic bronchopulmonary infections after lung transplantation. MATERIALS AND METHODS Forty-five episodes of opportunistic bronchopulmonary infection occurred in 27 (35%) of 77 lung transplant recipients during a 4-year period. Causative organisms, radiographic patterns, and mortality were reviewed. RESULTS Cytomegalovirus (CMV) was the most common pathogen (25 episodes), followed by Aspergillus species (seven episodes), Pneumocystis carinii (six episodes), herpes simplex virus (four episodes), Mycobacterium avium complex (two episodes), and M tuberculosis (one episode). Eighteen of the 25 episodes (72%) of CMV pneumonitis occurred in the first 4 months after transplantation; 24 (96%) occurred within the 1st year. Radiographic patterns of symptomatic CMV pneumonitis were diffuse haziness (60%), focal haziness (33%), and focal consolidation (7%). Aspergillus species locally invaded a necrotic bronchial anastomosis in three patients, each within 4 months of transplantation. P carinii was seen as focal haziness and caused no symptoms. Radiographic findings, when present, were seen almost exclusively in the transplanted lung. Despite three deaths attributable to opportunistic bronchopulmonary infection, the difference between the survival rates of patients with and those of patients without bronchopulmonary infection was not statistically significant (82% and 81%, respectively, 1 year after transplantation). CONCLUSION Opportunistic bronchopulmonary infections are common after lung transplantation. The most common pathogen is CMV, which causes diverse chest radiographic patterns. Opportunistic bronchopulmonary infections do not adversely affect overall mortality.
Stability Analysis of Two-Stage Stochastic Mathematical Programs with Complementarity Constraints via NLP Regularization

This paper presents numerical approximation schemes for a two-stage stochastic programming problem, where the second stage problem has a general nonlinear complementarity constraint. First the complementarity constraint is approximated by a parameterized system of inequalities with a well-known regularization approach by Scholtes [SIAM J. Optim. , 11 (2001), pp. 918–936] in deterministic mathematical programs with equilibrium constraints; the distribution of the random variables of the regularized two-stage stochastic program is then approximated by a sequence of probability measures. By treating the approximation problems as a perturbation of the original (true) problem, we carry out a detailed stability analysis of the approximated problems, including continuity and local Lipschitz continuity of optimal value functions and outer semicontinuity and continuity of the set of optimal solutions and stationary points. A particular focus is given to the case where the probability distribution is approximated by.
Ultrastructure of normal and degenerating glomerular terminals of dorsal root axons in the substantia gelatinosa of the rhesus monkey

The fine structure of primary sensory terminals within glomerular complexes of lamina II of Rexed (substantia gelatinosa Rolandi) in the spinal cord was investigated in normal adult rhesus monkeys and in monkeys subjected to thoracic or lumbosacral dorsal root transection. Three types “scalloped” primary sensory terminals were distinguished on the basis of their ultrastructural characteristics, size, and distribution of synaptic vesicle population: (1) dense sinusoid axon (DSA) terminals contain mediumsized (42–46 nm and 58–62 nm) and large (80 nm) clear synaptic vesicles; (2) large dense‐core vesicles (LDCV) terminals are equipped with empty synaptic vesicles ranging from 30 to 106 nm, large, (80 nm) and very large, (100 nm) dense‐core vesicles; and (3) regular synaptic vesicles (RSV) terminals contain a homogeneous population of 45–50 nm clear synaptic vesicles.
A Gentle Introduction to Machine Learning for Natural Language Processing: How to Start in 16 Practical Steps

We present a gentle introduction to machine learning in natural language processing. Our goal is to navigate readers through basic machine learning concepts and experimental techniques. As an illustrative example we practically address the task of word sense disambiguation using the R software system. We focus especially on students and junior researchers who are not trained in experimenting with machine learning yet and who want to start. To some extent, machine learning process is independent on both addressed task and software system used. Therefore readers who deal with tasks from different research areas or who prefer different software systems will gain useful knowledge as well.
Purification, characterization, and gene cloning of a chitinase from Stenotrophomonas maltophilia N4

The Stenotrophomonas maltophilia synthesises high‐activity chitinase in response to chitin or chitosan induction. The enzyme was purified 8.5 fold and subjected to characterisation. The optimum hydrolysis conditions for this enzyme when using colloidal chitin as substrate were pH 5.6 and temperature of 45 °C. The enzyme demonstrated high thermal stability at 45 °C within 2 h. The studied chitinase exhibited high activity towards colloidal chitin, glycol chitin and chitosan, while it did not hydrolyse glycosidic bonds in carboxymethylcellulose. The enzyme exhibited the highest activity, equalling 90 U/ml, towards Nitrophenyl β‐D‐N,N′,N″‐triacetylchitotriose and activity of 37 U/ml towards 4‐Nitrophenyl N,N′‐diacetyl‐β‐D‐chitobioside. The Km value in the presence of the two former substrates was:1.2 and 3.9 mM, respectively, which classifies the studied enzyme as an endochitinase. Cysteine and 2‐mercaptoethanol stimulated to a small degree the activity of the chitinase which may indicate the involvement of cysteine residues in the catalysis mechanism. The full length of the nucleotide sequence of this chitinase gene is 2106 bp, which amounts to 702 amino acids.
Inherited Immunoglobulin Idiotypes of the Mouse

A-CHO, group A streptococcal polysaccharide; cap; epsilon-aminocaproyl; Cg gene and Cj^ gene, the structural germ-line gene for the H chain or the L chain constant polypeptides; HPI, Haptenated Phage Inactivation method for detecting anti-hapten antibodies; IEF, isoelectric fociising; NBrP, (4-hydroxy-5-bromo-3-nitrophenyl) acetyl; NIP, (4-hydroxy-5-iodo-3-nitrophenyl) acetyl; NNP, (4-hydroxy-3, 5-dinitrophenyl) acetyl; NP, (4-hydroxy-3-nitrophenyl) acetyl; PC, phosphorylcholine; TMV, tobacco mosaic virus; V region, in this text, the part of an immunoglobulin molecule consisting of a Vg and a V^ domains or polypeptides (= Fy piece); Vg gene and V^ gene, structural germ line gene for the H chain or the L chain variable polypeptides.
Conceptions of Research: A phenomenographic study

This article reports on an investigation into the variation in how research is experienced by established senior researchers. It provides a new, discipline-neutral, non-technical framework for interpreting how academics are responding to the challenges of the changing context of higher education. The study identified four qualitatively different ways in which research is understood. These are differentiated according to whether they have an external product orientation or an internal process orientation; and whether the researchers themselves are in the forefront of their awareness or whether they appear to be incidental to their awareness. In the context of concern about the nature and role of research in the economy and about how it should be funded, and at a time when knowledge is said to be in crisis, the article suggests that the framework can contribute to rational analysis and decision-making.
Efficacy and safety of decitabine in combination with G-CSF, low-dose cytarabine and aclarubicin in newly diagnosed elderly patients with acute myeloid leukemia

Purpose This prospective phase II, open label, study was designed to assess the efficacy and safety of D-CAG induction treatment for elderly patients with newly diagnosed AML. Experimental Design All patients in this study were treated with decitabine of 15 mg/m2 for 5 days and G-CSF for priming, in combination with cytarabine of 10-mg/m2 q12h for 7 days and aclarubicin of 10 mg/day for 4 days (D-CAG). Results Among 85 evaluable patients, overall response rate (ORR) and complete remission (CR) were 82.4% and 64.7%, respectively, after 1 cycle of therapy. The ORR in patients aged <70 years was 83.0% and 81.6% in patients aged ≥70 years. There was a significantly longer median overall survival (OS) in patients with response (16 months) than in those without response (7 months, p< 0.0001). The OS for patients aged ≥70 years and 60-69 years was 10 months and 12 months, respectively (p=0.4994). The two-year OS probability was 19.2% and the twenty-month survival rate was 33.8%. Induction mortality of D-CAG treated elderly patients with AML is 4.4%. Conclusion D-CAG regimen was well tolerated and showed a promising clinic efficacy in elderly patients with AML (≥70 years).