Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographical delimitation of a partial selective sweep in African Drosophila melanogaster

Positive selection leaves characteristic footprints on DNA variation but detecting such patterns is challenging as the age, the intensity and the mode of selection as well as demography and evolutionary parameters (mutation and recombination rates) all play roles and these are difficult to disentangle. We recorded nucleotide variation in a sample of isogenic chromosomes from a western African population of Drosophila melanogaster at a locus (Fbp2) for which a partial selective sweep had previously been reported. We compared this locus to four other genes from the same chromosomes and from a European and an East African population. Then, we assessed Fbp2 variation in a sample of 370 chromosomes covering a comprehensive geographic sampling of 16 African localities. The signature of selection was tested while accounting for the demographic history of the populations. We found a significant signal of selection in two West African localities including Ivory Coast. Variation at Fpb2 would thus represent a case of an ongoing selective sweep in the range of this species. A weaker, nonsignificant, signal of selection was, however, apparent in some other populations, thus leaving open several possibilities: (i) the selective sweep originated in Ivory Coast and has spread to the rest of the continent; (ii) several African populations report the signature of a selective event having occurred in an ancestral population; (iii) this genome region is subject to independent selective events in African populations; and (iv) A neutral scenario with population subdivision and local bottleneck cannot be fully excluded to explain the molecular patterns observed in some populations.
A review on driver drowsiness based on image, bio-signal, and driver behavior

The ratio of accidents caused by drowsiness, increases slightly year by year. The most victims of this case are young adult and mostly happens in developed country. Therefore, to reduce the number of accidents caused by drowsiness, researchers around the world develope some methods for detecting drowsiness on driver's face automatically. They propose various features such as visual, non-visual, and vehicular. Visual features are extracted from driver's face and recorded by camera. Non-visual features are signals emerged from driver's body and to acquire those signals, they use special sensor attached to driver's body. Vehicular features are obtained by observing the behavior of driver during driving. From those features which are propsed by researchers, we discussed 3 ideas that can be considered as guidance to lead researcher in developing drowsiness detection. The first idea is creating the dataset of drowsiness facial expression because it can predict drowsiness and fatigue. Second idea is to combine visual, non-visual, and vehicular features into one for better detection. And last one is developing wearable hardwares such as smartwatch for drowsiness detection which are easy to use and user friendly.
Efficacy of biological disease-modifying antirheumatic drugs: a systematic literature review informing the 2013 update of the EULAR recommendations for the management of rheumatoid arthritis

Objectives To update the evidence for the efficacy of biological disease-modifying antirheumatic drugs (bDMARD) in patients with rheumatoid arthritis (RA) to inform the European League Against Rheumatism(EULAR) Task Force treatment recommendations. Methods Medline, Embase and Cochrane databases were searched for articles published between January 2009 and February 2013 on infliximab, etanercept, adalimumab, certolizumab-pegol, golimumab, anakinra, abatacept, rituximab, tocilizumab and biosimilar DMARDs (bsDMARDs) in phase 3 development. Abstracts from 2011 to 2012 American College of Rheumatology (ACR) and 2011–2013 EULAR conferences were obtained. Results Fifty-one full papers, and 57 abstracts were identified. The randomised controlled trials (RCT) confirmed the efficacy of bDMARD+conventional synthetic DMARDs (csDMARDs) versus csDMARDs alone (level 1B evidence). There was some additional evidence for the use of bDMARD monotherapy, however bDMARD and MTX combination therapy for all bDMARD classes was more efficacious (1B). Clinical and radiographic responses were high with treat-to-target strategies. Earlier improvement in signs and symptoms were seen with more intensive initial treatment strategies, but outcomes were similar upon addition of bDMARDs in patients with insufficient response to MTX. In general, radiographic progression was lower with bDMARD use, mainly due to initial treatment effects. Although patients may achieve bDMARD- and drug-free remission, maintenance of clinical responses was higher with bDMARD continuation (1B), but bDMARD dose reduction could be applied (1B). There was still no RCT data for bDMARD switching. Conclusions The systematic literature review confirms efficacy of biological DMARDs in RA. It addresses different treatment strategies with the potential for reduction in therapy, particularly with early disease control, and highlights emerging therapies.
Substrate induction of siderophore transport in Bacillus subtilis mediated by a novel one‐component regulator

When iron is scarce, Bacillus subtilis expresses genes involved in the synthesis and uptake of the siderophore bacillibactin (BB) and uptake systems to pirate other microbial siderophores. Here, we demonstrate that transcriptional induction of the feuABCybbA operon, encoding the Fe–BB uptake system, is mediated by Btr (formerly YbbB), which is encoded by the immediately upstream gene. Btr contains an AraC‐type DNA binding domain fused to a substrate binding protein (SBP) domain related to FeuA, the SBP for Fe–BB uptake. When cells are iron‐limited, the Fur‐mediated repression of btr is relieved and Btr binds to a conserved direct repeat sequence adjacent to feuA to activate transcription. If BB is present, Btr further activates feuA expression. Btr binds with high affinity to both apo–BB and Fe–BB, and the resulting complex displays a significantly increased efficacy as a transcriptional activator relative to Btr alone. Btr can also activate transcription in response to the structurally similar siderophore enterobactin, although genetic analyses indicate that the two siderophores make distinct interactions with the Btr substrate binding domain. Thus, the FeuABC transporter is optimally expressed under conditions of iron starvation, when Fur‐mediated repression is relieved, and in the presence of its cognate substrate.
Resistance of fluorescent‐labelled Actinobacillus actinomycetemcomitans strains to phagocytosis and killing by human neutrophils

Neutrophils are initially the predominant cells involved in the host defence of bacterial infections, including periodontal disease. Aggressive periodontitis is associated with Actinobacillus actinomycetemcomitans, a Gram‐negative capnophilic microorganism. Infections caused by A. actinomycetemcomitans are not resolved by the host immune response despite the accumulation of neutrophils at the site of inflammation. To better understand the role of natural host defence mechanisms in A. actinomycetemcomitans infections, the interaction of phenotypically diverse strains of this pathogen with human neutrophils was assessed directly using techniques such as genetic labelling with the gene for green fluorescent protein, fluorescence‐activated cell sorting and fluorescence imaging. The study included clinical isolates of A. actinomycetemcomitans represented by self‐aggregating, biofilm‐associated and isogenic planktonic variants. Data obtained showed that complement‐mediated phagocytosis of A. actinomycetemcomitans was generally inefficient regardless of strain‐specific serotype or leukotoxin production. Furthermore, the majority of ingested bacteria remained viable after exposure to neutrophils for 1 h. Interestingly, uptake of antibody‐opsonized bacteria resulted in the rapid cell death of neutrophils. This was in contrast to ingestion of complement‐opsonized bacteria, which did not affect neutrophil viability. The methods used in this study provided reliable and reproducible results with respect to adherence, phagocytosis and killing of A. actinomycetemcomitans when encountering human neutrophils.
Joint Sensing and Transmission for AF Relay Assisted PU Transmission in Cognitive Radio Networks

Recent measurements show that there are abundant spectrum opportunities across the licensed cellular bands, over which the relay stations (RSs) are widely employed for both coverage extension and throughput improvement. However, current efforts in cognitive radios focus on exploiting spectrum holes over the licensed direct transmission links. To exploit new spectrum opportunities over the licensed relay assisted transmission links, we propose a novel two-phase joint sensing and transmission scheme (TP-JSTS) for the dual-hop Amplify-and-Forward (AF) relay assisted primary user (PU) transmission in cognitive radio networks. The TP-JSTS takes into account the relay behaviors of the PU system. In the first phase, the secondary user (SU) senses the signal transmitted by the PU base station (BS). In the second phase, the SU detects the signals sent by the PU-Relays. To protect the PU from harmful interference, the SU transmits within the current band in the rest of each phase only when the PU is detected to be absent. We investigate the sensing performance, throughput performance and delay performance of our proposed TP-JSTS when all the PU-Relays adopt the AF relay protocol. We obtain the optimal sensing-time allocation strategy that maximizes the achievable throughput of the SU and the optimal sensing-time allocation strategy that minimizes the average transmission delay of the SU. Simulation results show that there exists an optimal pair of sensing-time durations that maximizes the achievable throughput for the SU, while there exists another optimal pair of sensing-time durations that minimizes the average transmission delay for the SU.
Functional expression of transgenic α1sDHPR channels in adult mammalian skeletal muscle fibres

Non‐technical summary In mammalian skeletal muscle, the coupling between action potential activation and contraction is supposed to be ultimately mediated by the interaction of two ion channels, the L‐type calcium channel (so‐called dihydropyridine receptor channel) at the transverse tubular system, and the sarcoplasmic reticulum (SR) calcium release channel (so‐called ryanodine receptor channel). This paper demonstrates that adult skeletal muscle fibres transfected in vivo with DNA plasmids are able to express functional transgenic dihydropyridine receptor channels. More importantly, the data suggest that transgenic dihydropyridine receptor channels replace native channels in their interaction with SR calcium release channels. Our findings open new avenues for structural and functional studies of the molecular interactions underlying excitation–contraction coupling within the physiologically relevant cellular context of adult mammalian skeletal muscle fibres.
Influence of polymorphisms in genes encoding immunoregulatory proteins and metabolizing enzymes on susceptibility and outcome in patients with diffuse large B-cell lymphoma treated with rituximab

Abstract We analyzed the allelic distribution of 12 candidate polymorphisms in a large retrospective study of 486 patients with diffuse large B-cell lymphoma (DLBCL) treated at Oslo University Hospital with 1056 blood donors serving as controls. Variants in TNFα (rs1800629) (GG vs. AG/AA, p < 0.001) and LTA (rs909253) (AA vs. AG/GG, p = 0.02) and deletions in GSTM1 and GSTT1 (undeleted vs. deleted, p = 0.01 and p = 0.01, respectively) were associated with increased susceptibility of developing DLBCL. IL-10 (rs1800896) variants (GG vs. AG/AA, p = 0.03) were associated with decreased susceptibility. In line with several previous reports, patients carrying the TNFα (rs1800629) A allele treated in the pre-rituximab era had inferior outcome compared to patients carrying the homozygous GG genotype (p = 0.004, n = 33). However, patients receiving at least one dose of rituximab had equal outcome regardless of their TNFα genotype (HR = 0.94, p = 0.79, n = 307). Deletion in GSTM1 was associated with inferior outcome for patients with low International Prognostic Index (IPI) score (p = 0.04). Our findings support the suggestions that polymorphisms in genes encoding immunoregulatory proteins and enzymes that metabolize carcinogens and chemotherapeutic drugs influence DLBCL susceptibility and possibly treatment outcome. The influence of polymorphisms in immunoregulatory genes on outcome in DLBCL should be reevaluated in the rituximab era.
Calculation of hybrid multi-layered perceptron neural network output using matrix multiplication

After some studies on the HMLP neural network output equation, it was found out that parts of the equation resemble matrix multiplication operation. Therefore, an approach to calculate the output equation of the HMLP using matrix multiplication method was proposed. The proposed approach was simulated and compared with another approach to calculate HMLP output using loops. The result proved that the output of the HMLP calculated using matrix multiplication method is the same as when being calculated using looping method. When comparing the processing time of both methods, the matrix multiplication method is faster than looping method for HMLP with more nodes. However, looping method calculated the output faster for HMLP with less nodes. This paper presents part of an ongoing study with the goal to develop an architecture for implementing the HMLP on FPGA.
Catholic Reform From Cardinal Ximenes to the Council of Trent 1495-1563.John C. Olin

and power; the proper uses of deceit; war and the military; and the role of religion in the state. The anti-Machiavellians also dealt with a topic virtually ignored by Machiavelli, economic development. Finally, they developed a distinctive philosophy of history that emphasized the role of divine providence. In his concluding chapter Bireley shows how the views of the anti-Machiavellians reflect specific aspects of CounterReformation and Baroque culture. In assessing their significancetie maintains that their efforts to develop a Catholic statecraft represented part of the Church's overall effort to accommodate itself to a changing world. The anti-Machiavellians also demonstrated that politics was a worthy vocation for a Christian and thus helped revive the classical concept of politics as an honorable activity reserved for persons of ability and moral virtue. Bireley has written a truly impressive work on an important yet neglected subject. The book includes illustrations taken from the actual works of the anti-Machiavellians, informative endnotes, and an extensive bibliography of primary and secondary sources. The Counter-Reformation Prince represents a major contribution to the history of political thought and practice in early modern Europe. S T A T E U N I V E R S I T Y OF N E W YORK, Thomas I. Crimando
The obviousness rejection as a barrier to vaccine patent prosecution

After the US Supreme court’s KSR case, the trends for obvious and non-obvious rulings in terms of the CAFC decisions significantly increased and decreased, respectively. In re Kubin case, the invention disclosed the isolation and sequences of a polynucleotide that encodes a Natural Killer Cell Activation Inducing Ligand (NAIL) polypeptide. The soluble NAIL polypeptides could serve as an adjuvant in combination with vaccines. However, the appellants employed conventional methods to isolate a cDNA encoding NAIL and determine the cDNA’s full nucleotide sequence. Thus, the CAFC affirmed that a skilled artisan has a reasonable expectation of success in deriving the claimed invention in light of the teachings of the prior art. Based on this investigation, developers of human vaccines should contemplate the obvious barrier to patent prosecution. Furthermore, we also need to follow up the CAFC’s decision on the patentability of the isolated DNA containing sequence. A CAFC dissenting opinion stressed that the difference between an isolated DNA sequence and the product occurring in nature is just in the isolated form. Such a patent would not be “markedly different characteristics from any found in nature. ”
The relationship between working memory capacity and broad measures of cognitive ability in healthy adults and people with schizophrenia.

OBJECTIVE Working memory (WM) capacity, typically measured with cognitively complex span tasks, is correlated with higher order cognitive abilities in healthy adults. The goals of this study were to determine whether a more focused measure of visual WM storage capacity would show similar higher order ability correlations in healthy adults and in people with schizophrenia (PSZ), thereby demonstrating the importance of simple storage capacity; determine whether the illness alters the pattern of correlations across cognitive domains; and evaluate whether between-groups differences in WM capacity could account for the generalized cognitive impairment in PSZ. METHOD Ninety-nine PSZ and 77 healthy controls (HCs) completed a visual WM change-localization task, the Wechsler Abbreviated Scale of Intelligence (WASI), and the MATRICS Consensus Cognitive Battery (MCCB). RESULTS PSZ performed more poorly than HCs on all cognitive measures. The between-groups effect size for WM capacity was large (d = 1.11). WM robustly correlated with WASI and MCCB performance, with no significant differences in the magnitude or pattern of correlations across groups. When the groups were pooled, WM capacity correlated at r = . 68 with MCCB composite score and at r = . 56 with WASI estimated Full Scale IQ. WM capacity accounted for approximately 40% of the between-groups variance across the WASI and MCCB. CONCLUSIONS A simple measure of WM storage capacity is robustly associated with the higher order cognitive abilities assessed by the WASI and MCCB in HCs and PSZ. WM capacity reduction may be a critical determinant of the general cognitive impairment in PSZ.
Neurocognitive Impairment of Mental Rotation in Major Depressive Disorder: Evidence From Event-Related Brain Potentials

Abstract Mental rotation performance may be used as an index of mental slowing or bradyphrenia and may reflect speed of motor preparation. Previous studies suggest that major depressive disorder (MDD) presents correlates of impaired behavioral performance for mental rotation and psychomotor disturbance. Very little is known about the electrophysiological mechanism underlying this deficit. The present study was the first to investigate the event-related brain potential (ERP) correlates of mental rotation and their mental slowing or bradyphrenia in MDD. ERPs were recorded while we tested 25 MDD patients and 26 healthy controls by evaluating the performance of MDD patients on hand and letter rotation tasks at different orientations, and their 400-to-600-msec time window was measured and analyzed for latencies and peak amplitudes over the electrodes. First, individuals with MDD were slower and made more errors in mentally rotating hands and letters than healthy controls did, and individuals with MDD exhibited a greater difference in response times and errors than controls did between hands and letters. Second, the mean peak amplitude was significantly lower and the mean latency was significantly longer in the 400-to-600-msec time window at the parietal site in the hand tasks in MDD patients than in controls, but this was not seen in the letter task, with only lower mean peak amplitude. MDD patients present the absence of a typical mental rotation function for the amplitude of the rotation-related negativity in the hand and letter tasks. Third, the scalp activity maps in MDD patients exhibited the absence of activation in the left parietal site for the mental rotation of hands, as shown in healthy participants. In contrast, their brain activation for the letter task was similar to those of healthy participants. These data suggest that mental imagery of hands and letters relies on different cognitive and neural mechanisms and indicate that the left posterior parietal lobe is a necessary structure for mental transformations of human hands. Importantly, MDD deficits were more seriously present specific to the hands than the letters. Such impairment may also be an important and possibly defining marker of MDD in particular.
Herpes simplex virus thymidine kinase transcripts are absent from both nucleus and cytoplasm during infection in the presence of cycloheximide

Nick-translated DNA from a recombinant plasmid containing the herpes simplex virus type 1 thymidine kinase gene was used as a probe for the synthesis of thymidine kinase RNA. The recombinant plasmid was generated by inserting the 3.5-kilobase fragment derived by BamHI digestion of herpes simplex virus type 1 DNA into plasmid pBR322. At 8 h after infection, cytoplasmic and nuclear RNA hybridized to 14% and 19% of the recombinant DNA probe, respectively. However, no significant hybridization was found with either nuclear or cytoplasmic RNA extracted from cells infected and maintained in the presence of cycloheximide. This suggests that no thymidine kinase-related RNA was synthesized in the absence of alpha polypeptides, and supports the hypothesis that the alpha polypeptides effect new thymidine kinase RNA synthesis rather than being involved in processing or transport of thymidine kinase RNA. In cells infected and maintained in the presence of the arginine analog canavanine, about 2 to 3% of the plasmid DNA was found to hybridize with cytoplasmic and nuclear RNA. However, when a recombinant plasmid DNA containing only thymidine kinase coding sequences was used, no significant hybridization was found. The inhibition of thymidine kinase transcription by canavanine suggests that thymidine kinase belongs to the beta 2 kinetic class.
Evaluation of Exhaled Nitric Oxide in Schoolchildren at Different Exhalation Flow Rates

Nitric oxide (NO) in exhaled air is believed to reflect allergic inflammation in the airways. Measured levels of exhaled NO vary with the exhaled flow rate, which therefore must be standardized. The aim of this study was to estimate the optimal exhalation flow rate when measuring NO in exhaled air. We studied 15 asthmatic children (8-18 y) with elevated NO levels and 15 age-matched controls and focused on how the quality of the NO curve profile, the discriminatory power, and the reproducibility were influenced by the exhalation flow rate. We used an on-line system for NO measurements at six different exhalation flow rates in the interval of 11-382 mL/s. The fraction of exhaled nitric oxide (FENO) was highly flow-dependent as was expected. Intermediate flow rates yielded a flat and stable NO plateau and were considerably easier to interpret than those obtained at the highest and lowest flow rates. The ratio of FENO between asthmatics and controls was lower at higher flow rates and a considerable overlap in NO values was demonstrated at all flow rates except 50 mL/s. The reproducibility was much lower at more extreme flow rates and was best at 50 mL/s. We conclude that a target exhalation flow rate of approximately 50 mL/s is to be preferred using the single-breath method for on-line NO measurements in schoolchildren.