Miracle-dz/UniFAR-FTUs huggingface dataset:
BELTracker: evidence sentence retrieval for BEL statements

Biological expression language (BEL) is one of the main formal representation models of biological networks. The primary source of information for curating biological networks in BEL representation has been literature. It remains a challenge to identify relevant articles and the corresponding evidence statements for curating and validating BEL statements. In this paper, we describe BELTracker, a tool used to retrieve and rank evidence sentences from PubMed abstracts and full-text articles for a given BEL statement (per the 2015 task requirements of BioCreative V BEL Task). The system is comprised of three main components, (i) translation of a given BEL statement to an information retrieval (IR) query, (ii) retrieval of relevant PubMed citations and (iii) finding and ranking the evidence sentences in those citations. BELTracker uses a combination of multiple approaches based on traditional IR, machine learning, and heuristics to accomplish the task. The system identified and ranked at least one fully relevant evidence sentence in the top 10 retrieved sentences for 72 out of 97 BEL statements in the test set. BELTracker achieved a precision of 0.392, 0.532 and 0.615 when evaluated with three criteria, namely full, relaxed and context criteria, respectively, by the task organizers. Our team at Mayo Clinic was the only participant in this task. BELTracker is available as a RESTful API and is available for public use. Database URL: http://www.openbionlp. org:8080/BelTracker/finder/Given_BEL_Statement
Comparative study on normalization procedures for cluster analysis of gene expression datasets

Normalization before clustering is often needed for proximity indices, such as Euclidian distance, which are sensitive to differences in the magnitude or scales of the attributes. The goal is to equalize the size or magnitude and the variability of these features. This can also be seen as a way to adjust the relative weighting of the attributes. In this context, we present a first large scale data driven comparative study of three normalization procedures applied to cancer gene expression data. The results are presented in terms of the recovering of the true cluster structure as found by five different clustering algorithms.
Dual peroxidase and colloidal gold-labeling study of angiotensin converting enzyme and angiotensin-like immunoreactivity in the rat subfornical organ

The cellular relationships between angiotensin converting enzyme (ACE) (EC 3.4.14.1) and angiotensin-like immunoreactivity (AGLI) were examined in the subfornical organ (SFO). Brains from adult rats were fixed by vascular perfusion with 3.75% acrolein and 2% paraformaldehyde. The region containing the SFO was then sectioned on a vibrating microtome. Partially permeabilized sections were immunocytochemically labeled using the peroxidase-antiperoxidase (PAP) or combined PAP and immunogold methods. Goat antiserum to ACE was localized to both non-neuronal and neuronal cells within the SFO. Intense peroxidase immunoreactivity for ACE was associated with the ventricular and basal surface of ependymal cells, the luminal surface of the vascular endothelium, portions of glial membranes exposed to extracellular spaces, and membranous organelles within neuronal processes. Two antisera raised in rabbits against angiotensin II showed peroxidase immunoreactivity within the extracellular spaces and throughout the cytoplasm of numerous axon terminals and a few perikarya and dendrites in the SFO. Axon terminals and dendrites also showed aggregates of AGLI in smooth membranes and vesicles near the plasmalemma. Gold labeling for AGLI was evident in only 6% of the axon terminals and in a smaller number of dendrites containing peroxidase immunoreactivity for ACE. The low incidence of terminals containing both markers appeared to at least partially reflect limited penetration of the 10 nm gold particles. These results provide the first ultrastructural evidence that ACE is associated with the plasmalemma and membranous organelles strategically located for interaction with precursors of angiotensin II or other peptides within the cerebrospinal fluid, extracellular spaces and neurons of the SFO.
HSP90 inhibitors decrease AID levels and activity in mice and in human cells

Activation induced deaminase (AID) initiates somatic hypermutation and class switch recombination of the Ig genes in antigen‐activated B cells, underpinning antibody affinity maturation and isotype switching. AID can also be pathogenic by contributing to autoimmune diseases and oncogenic mutations. Moreover, AID can exert noncanonical functions when aberrantly expressed in epithelial cells. The lack of specific inhibitors prevents therapeutic applications to modulate AID functions. Here, we have exploited our previous finding that the HSP90 molecular chaperoning pathway stabilizes AID in B cells, to test whether HSP90 inhibitors could target AID in vivo. We demonstrate that chronic administration of HSP90 inhibitors decreases AID protein levels and isotype switching in immunized mice. HSP90 inhibitors also reduce disease severity in a mouse model of acute B‐cell lymphoblastic leukemia in which AID accelerates disease progression. We further show that human AID protein levels are sensitive to HSP90 inhibition in normal and leukemic B cells, and that HSP90 inhibition prevents AID‐dependent epithelial to mesenchymal transition in a human breast cancer cell line in vitro. Thus, we provide proof‐of‐concept that HSP90 inhibitors indirectly target AID in vivo and that endogenous human AID is widely sensitive to them, which could have therapeutic applications.
CpG domains downstream of TSSs promote high levels of gene expression

CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. Here, we demonstrate that intragenic CpG frequency and distribution impacts transgene and genomic gene expression levels in mammalian cells. As shown for the Macrophage Inflammatory Protein 1α, de novo RNA synthesis correlates with the number of CpG dinucleotides, whereas RNA splicing, stability, nuclear export and translation are not affected by the sequence modification. Differences in chromatin accessibility in vivo and altered nucleosome positioning in vitro suggest that increased CpG levels destabilize the chromatin structure. Moreover, enriched CpG levels correlate with increased RNA polymerase II elongation rates in vivo. Interestingly, elevated CpG levels particularly at the 5′ end of the gene promote efficient transcription. We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. We suggest that these 5′ CpG domains are required to distort the chromatin structure and to increase gene activity.
Minigames for Mental Health: Improving Warfighters' Coping Skills and Awareness of Mental Health Resources.

OBJECTIVE Providing resources and stress management techniques is vital to the improvement of mental health outcomes of deploying warfighters. Despite the large amount of resources available, they are largely ineffective owing in part to lack of familiarity and knowledge of the resources themselves. This may be ameliorated through game-based practice environments. The objective of this study was to develop and evaluate a serious game to teach deploying military personnel about available mental health resources and coping skills, as well as to determine whether the inclusion of minigames improved learning outcomes. MATERIALS AND METHODS Participants played the serious game "Walk in My Shoes" (Novonics Corp., Orlando, FL) to learn about mental health resources and coping skills. Half of the participants applied this knowledge during the game by playing minigames, whereas the other half played minigames featuring irrelevant content. This study was conducted both in-person and online. RESULTS Participants who practiced the content by playing relevant minigames had positive learning gains, whereas those who played minigames with irrelevant content did not improve from baseline. There were no differences with respect to whether the game was played in the laboratory or in a more naturalistic environment. CONCLUSIONS Web-based serious games can be effective in providing information about resources and skills to deploying warfighters. Including minigames to provide practice in a game-based training environment such as a serious game improves learning outcomes. Such a serious game, regardless of the inclusion of minigames, also increases self-reports of deployment self-efficacy.
Bergman metrics and geodesics in the space of K

A guiding principle in Kahler geometry is that the infinite dimensional sym- metric space H of Kahler metrics in a fixed Kahler class on a polarized projective Kahler manifold M should be well approximated by finite dimensional submanifolds Bk ⊂ H of Bergman metrics of height k (Yau, Tian, Donaldson). The Bergman metric spaces are sym- metric spaces of type GC/G where G = U(dk +1) for certain dk. This article establishes the basic estimates for Bergman approximations for geometric families of toric Kahler manifolds. The approximation results are applied to the endpoint problem for geodesics of H, which are solutions of a homogeneous complex Monge-Ampere equation in A × X, where A ⊂ C is an annulus. Donaldson, Arezzo-Tian and Phong-Sturm raised the question whether H- geodesics with fixed endpoints can be approximated by geodesics of Bk. Phong-Sturm proved weak C 0 -convergence of Bergman to Monge-Ampere geodesics on a general Kahler manifold. Our approximation results show that one has C 2 (A × X) convergence in the case of toric Kahler metrics, extending our earlier result on CP 1 . In subsequent papers, the techniques of this article are applied to approximations for harmonic maps into H, to test configuration geodesic rays and to the smooth initial value problem.
Effect of carbohydrate ingestion and ambient temperature on muscle fatigue development in endurance-trained male cyclists.

The aim of the present study was to determine the effect of carbohydrate (CHO; sucrose) ingestion and environmental heat on the development of fatigue and the distribution of power output during a 16.1-km cycling time trial. Ten male cyclists (Vo(2max) = 61.7 +/- 5.0 ml.kg(-1). min(-1), mean +/- SD) performed four 90-min constant-pace cycling trials at 80% of second ventilatory threshold (220 +/- 12 W). Trials were conducted in temperate (18.1 +/- 0.4 degrees C) or hot (32.2 +/- 0.7 degrees C) conditions during which subjects ingested either CHO (0.96 g.kg(-1). h(-1)) or placebo (PLA) gels. All trials were followed by a 16.1-km time trial. Before and immediately after exercise, percent muscle activation was determined using superimposed electrical stimulation. Power output, integrated electromyography (iEMG) of vastus lateralis, rectal temperature, and skin temperature were recorded throughout the trial. Percent muscle activation significantly declined during the CHO and PLA trials in hot (6.0 and 6.9%, respectively) but not temperate conditions (1.9 and 2.2%, respectively). The decline in power output during the first 6 km was significantly greater during exercise in the heat. iEMG correlated significantly with power output during the CHO trials in hot and temperate conditions (r = 0.93 and 0.73; P < 0.05) but not during either PLA trial. In conclusion, cyclists tended to self-select an aggressive pacing strategy (initial high intensity) in the heat.
Absorption, distribution, metabolism and excretion (ADME) of the ALK inhibitor alectinib: results from an absolute bioavailability and mass balance study in healthy subjects

Abstract 1. Alectinib is a highly selective, central nervous system-active small molecule anaplastic lymphoma kinase inhibitor. 2. The absolute bioavailability, metabolism, excretion and pharmacokinetics of alectinib were studied in a two-period single-sequence crossover study. A 50 μg radiolabelled intravenous microdose of alectinib was co-administered with a single 600 mg oral dose of alectinib in the first period, and a single 600 mg/67 μCi oral dose of radiolabelled alectinib was administered in the second period to six healthy male subjects. 3. The absolute bioavailability of alectinib was moderate at 36.9%. Geometric mean clearance was 34.5 L/h, volume of distribution was 475 L and the hepatic extraction ratio was low (0.14). 4. Near-complete recovery of administered radioactivity was achieved within 168 h post-dose (98.2%) with excretion predominantly in faeces (97.8%) and negligible excretion in urine (0.456%). Alectinib and its major active metabolite, M4, were the main components in plasma, accounting for 76% of total plasma radioactivity. In faeces, 84% of dose was excreted as unchanged alectinib with metabolites M4, M1a/b and M6 contributing to 5.8%, 7.2% and 0.2% of dose, respectively. 5. This novel study design characterised the full absorption, distribution, metabolism and excretion properties in each subject, providing insight into alectinib absorption and disposition in humans.
Unsupervised Domain Adaptation by Backpropagation

Top-performing deep architectures are trained on massive amounts of labeled data. In the absence of labeled data for a certain task, domain adaptation often provides an attractive option given that labeled data of similar nature but from a different domain (e.g. synthetic images) are available. Here, we propose a new approach to domain adaptation in deep architectures that can be trained on large amount of labeled data from the source domain and large amount of unlabeled data from the target domain (no labeled target-domain data is necessary). As the training progresses, the approach promotes the emergence of "deep" features that are (i) discriminative for the main learning task on the source domain and (ii) invariant with respect to the shift between the domains. We show that this adaptation behaviour can be achieved in almost any feed-forward model by augmenting it with few standard layers and a simple new gradient reversal layer. The resulting augmented architecture can be trained using standard backpropagation. Overall, the approach can be implemented with little effort using any of the deep-learning packages. The method performs very well in a series of image classification experiments, achieving adaptation effect in the presence of big domain shifts and outperforming previous state-of-the-art on Office datasets.
Molecular Characterization of the α-Glucosidase Gene (malA) from the Hyperthermophilic ArchaeonSulfolobus solfataricus

ABSTRACT Acidic hot springs are colonized by a diversity of hyperthermophilic organisms requiring extremes of temperature and pH for growth. To clarify how carbohydrates are consumed in such locations, the structural gene (malA) encoding the major soluble α-glucosidase (maltase) and flanking sequences fromSulfolobus solfataricus were cloned and characterized. This is the first report of an α-glucosidase gene from the archaeal domain. malA is 2,083 bp and encodes a protein of 693 amino acids with a calculated mass of 80.5 kDa. It is flanked on the 5′ side by an unusual 1-kb intergenic region. Northern blot analysis of themalA region identified transcripts for malA and an upstream open reading frame located 5′ to the 1-kb intergenic region. The malA transcription start site was located by primer extension analysis to a guanine residue 8 bp 5′ of themalA start codon. Gel mobility shift analysis of themalA promoter region suggests that sequences 3′ to position −33, including a consensus archaeal TATA box, play an essential role in malA expression. malA homologs were detected by Southern blot analysis in other S. solfataricus strains and in Sulfolobus shibatae, while no homologs were evident in Sulfolobus acidocaldarius, lending further support to the proposed revision of the genus Sulfolobus. Phylogenetic analyses indicate that the closest S. solfataricusα-glucosidase homologs are of mammalian origin. Characterization of the recombinant enzyme purified from Escherichia colirevealed differences from the natural enzyme in thermostability and electrophoretic behavior. Glycogen is a substrate for the recombinant enzyme. Unlike maltose hydrolysis, glycogen hydrolysis is optimal at the intracellular pH of the organism. These results indicate a unique role for the S. solfataricus α-glucosidase in carbohydrate metabolism.
Receiver Multiuser Diversity Aided Multi-Stage Minimum Mean-Square Error Detection for Heavily Loaded DS-CDMA and SDMA Systems

By investigating the conditions required for successive interference cancellation multiuser detectors (SIC-MUD) to achieve near-optimum BER performance, we propose and investigate a so-called receiver multiuser diversity aided multi-stage minimum mean-square error MUD (RMD/MS-MMSE MUD), which is operated in the SIC principles. The BER performance of the RMD/MS-MMSE MUD is investigated in association with both the direct-sequence code-division multiple-access (DS-CDMA) over either Gaussian or Rayleigh fading channels, and the space-division multiple-access (SDMA) over Rayleigh fading channels. Furthermore, we consider both full-load and overload scenarios in comparison with the spreading factor N of DS-CDMA and the number of receive antennas N in SDMA. Our studies show that the RMD/MS-MMSE MUD is highly efficient for both full-load and overload systems. Specifically, the RMD/MS-MMSE MUD for the full-load systems of moderate size is capable of attaining the BER performance similar to that of the optimum maximum likelihood MUD (ML-MUD). For the overload systems, it can allow a DS-CDMA or SDMA system to support K=2N users and still achieve much better BER performance than a corresponding DS-CDMA or SDMA system using conventional MMSE-MUD to support K=N users.
Decoding Faces: The Contribution of Self- Expressiveness Level and Mimicry Processes to Emotional Understanding

Facial expressions provide valuable information in making judgments about internal emotional states. Evaluation of facial expressions can occur through mimicry processes via the mirror neuron system (MNS) pathway, where a decoder mimics a target’s facial expression and proprioceptive perception prompts emotion recognition. Female participants rated emotional facial expressions when mimicry was inhibited by immobilization of facial muscles and when mimicry was uncontrolled, and were evaluated for self-expressiveness level. A mixed ANOVA was conducted to determine how self-expressiveness level and manipulation of facial muscles impacted recognition accuracy for facial expressions. Main effects of self-expressiveness level and facial muscle manipulation were not found to be significant (p > .05), nor did these variables appear to interact (p > .05). The results of this study suggest that an individual’s selfexpressiveness level and use of mimicry processes may not play a central role in emotion recognition.
The Effects of Mother Tongue and Text Difficulty on Gaze Behaviour while Reading Afrikaans Text

Reading is done by the coordinated execution of a number of processes, e.g. decoding, lexical access, assigning semantic roles and relating information across sentences. Visual inspection of raw gaze data was done to analyse the gaze behaviour of first (L1) and second language (L2) readers of Afrikaans text. Some of the known gaze behaviours in other languages were confirmed for L1 readers but it was found that L2 readers do not exhibit the typical gaze behaviours. L2 readers use more fixations than L1 readers to read the same text. Individual fixations of L2 readers are longer than that of L1 readers. It was also shown that the perceived difficulties of L2 readers are more pronounced with difficult texts than with easy texts. Specific examples are given that display the differences between easy and difficult reading pieces.
Analysis of random and burst error codes in 2-state Markov channels

Markov chains are a popular means to capture correlated random processes for characterization and analysis of error pattern or bursty traffic in data transmission. The performance evaluation of communication protocols based on Markov models is tractable with limited state space and often depends on efficient implementation. Simulation or other methods have to be adopted for system of higher complexity. We study the effect of bit errors on transmitted packets for Markov error processes in the presence of error detecting or error correcting codes. We show that the evaluation for 2-state Markov channels leads the same 2-state channel characteristics also for packet errors, where parameters are determined by a recursive and closed form solution depending on the parameters of the bit error channel. Computation schemes are derived for random and burst error detecting and correcting codes whose computation effort is shown to be moderate and generally tractable for usual packet sizes in telecommunication.
Riverine fish diversity varies according to geographical isolation and land use modification

Abstract Understanding the environmental factors driving species‐genetic diversity correlations (SGDCs) is critical for designing appropriate conservation and management strategies to protect biodiversity. Yet, few studies have explored the impact of changing land use patterns on SGDCs specifically in aquatic communities. This study examined patterns of genetic diversity in roach (Rutilus rutilus L.) together with fish species composition across 19 locations in a large river catchment, spanning a gradient in land use. Our findings show significant correlations between some, but not all, species and genetic diversity end points. For example, genetic and species differentiation showed a weak but significant linear relationship across the Thames catchment, but additional diversity measures such as allelic richness and fish population abundance did not. Further examination of patterns in species and genetic diversity indicated that land use intensification has a modest effect on fish diversity compared to the combined influence of geographical isolation and land use intensification. These results indicate that environmental changes in riparian habitats have the potential to amplify shifts in the composition of stream fish communities in poorly connected river stretches. Conservation and management strategies for fish populations should, therefore, focus on enhancing connectivity between river stretches and limit conversion of nearby land to arable or urban use to maintain current levels of biodiversity.
Is there a trade-off between clutch size and egg volume in Magpie Pica pica in northwestern Croatia?

A negative relationship, or trade-off, between egg size (egg volume or egg mass) and clutch size is a central component of life-history theory. This paper presents evidence for a relationship between clutch size and egg volume (egg size) of the Magpie (Pica pica). Magpies are common and sedentary birds in study area. Egg characteristics were recorded in Mokrice rural area (46°00’N, 15°55’E), northwestern Croatia; carried out during the breeding season (April–May) in the year 2012. I have not detected any negative correlation (trade-off) between mean estimated egg volume (egg size) and clutch size in the Magpie. The results indicate that, in researched Magpie population, in northwestern Croatia, there is a positively significant correlation between clutch size and egg volume. It can probably be explained by good environmental conditions and/or good quality females, which other authors offer as a plausible explanation. In conclusion, these results do not seem to support the prediction based on the theory of optimal egg/clutch size concerning the inverse relationship between egg size and clutch size.