Miracle-dz/UniFAR-FTUs huggingface dataset:
Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review

MOTIVATION Techniques that are capable of automatically analyzing the information structure of scientific articles could be highly useful for improving information access to biomedical literature. However, most existing approaches rely on supervised machine learning (ML) and substantial labeled data that are expensive to develop and apply to different sub-fields of biomedicine. Recent research shows that minimal supervision is sufficient for fairly accurate information structure analysis of biomedical abstracts. However, is it realistic for full articles given their high linguistic and informational complexity? We introduce and release a novel corpus of 50 biomedical articles annotated according to the Argumentative Zoning (AZ) scheme, and investigate active learning with one of the most widely used ML models-Support Vector Machines (SVM)-on this corpus. Additionally, we introduce two novel applications that use AZ to support real-life literature review in biomedicine via question answering and summarization. RESULTS We show that active learning with SVM trained on 500 labeled sentences (6% of the corpus) performs surprisingly well with the accuracy of 82%, just 2% lower than fully supervised learning. In our question answering task, biomedical researchers find relevant information significantly faster from AZ-annotated than unannotated articles. In the summarization task, sentences extracted from particular zones are significantly more similar to gold standard summaries than those extracted from particular sections of full articles. These results demonstrate that active learning of full articles' information structure is indeed realistic and the accuracy is high enough to support real-life literature review in biomedicine. AVAILABILITY The annotated corpus, our AZ classifier and the two novel applications are available at http://www.cl. cam.ac. uk/yg244/12bioinfo.html
Integrated SVC and step-down transformer model for Newton-Raphson load flow studies

This letter presents an integrated static VAr compensator (SVC) and step-down transformer model suitable for power flow studies using the Newton-Raphson method. The SVC is taken to be a continuous, variable-shunt susceptance that is adjusted automatically to satisfy a specified voltage magnitude. The step-down transformer is represented by an admittance that combines easily with the variable susceptance, representing the SVC plant. The resulting equivalent model allows for a direct SVC voltage regulation at the high-voltage side of the transformer, which does not compromise the quadratic convergence characteristics of the Newton-Raphson method.
A Model of Manual Control with Perspective Scene Viewing

A model of manual control during perspective scene viewing is presented, which combines the Crossover Model with a simplied model of perspective-scene viewing and visualcue selection. The model is developed for a particular example task: an idealized constantaltitude task in which the operator controls longitudinal position in the presence of both longitudinal and pitch disturbances. An experiment is performed to develop and validate the model. The model corresponds closely with the experimental measurements, and identied model parameters are highly consistent with the visual cues available in the perspective scene. The modeling results indicate that operators used one visual cue for position control, and another visual cue for velocity control (lead generation). Additionally, operators responded more quickly to rotation (pitch) than translation (longitudinal).
Early onset of inflammation and later involvement of TGFβ in Duchenne muscular dystrophy

Objective: To identify stage-specific induction of molecular pathology pathways in Duchenne muscular dystrophy (DMD). Methods: We performed mRNA profiling using muscles from fetopsies, infants (aged 8 to 10 months), and symptomatic patients (aged 5 to 12 years) with DMD, and age- and sex-matched controls. We performed immunohistochemistry to determine changes at the protein level and protein localization. Results: Activated tissue dendritic cells, expression of toll-like receptor 7, and strong induction of nuclear factor-κB pathways occurred soon after birth in DMD muscle. Two muscle wasting pathways, atrogin-1 and myostatin, were not induced at any stage of the disease. Normal muscle showed accumulation of glycolytic and oxidative metabolism capacity with increased age, but this accumulation failed in DMD. The transforming growth factor (TGF)-β pathway was strongly induced in symptomatic patients, with expression of TGFβ type II receptor and apoptosis signal-regulating kinase 1 proteins on subsets of mature DMD myofibers Conclusions: Our data show stage-specific remodeling of human dystrophin-deficient muscle, with inflammatory pathways predominating in the presymptomatic stages and acute activation of TGFβ and failure of metabolic pathways later in the disease.
Long-Acting Risperidone and Oral Antipsychotics in Schizophrenia

1. Zoungas S, de Galan BE, Ninomiya T, et al. Combined effects of routine blood pressure lowering and intensive glucose control on macrovascular and microvascular outcomes in patients with type 2 diabetes: new results from the ADVANCE trial. Diabetes Care 2009;32:2068-74. 2. ADVANCE Collaborative Group. Intensive blood glucose control and vascular outcomes in patients with type 2 diabetes. N Engl J Med 2008;358:2560-72. 3. de Galan BE, Tack CJ, Lenders JW, et al. Theophylline improves hypoglycemia unawareness in type 1 diabetes. Diabetes 2002;51:790-6.
Interactions of Prototype Foamy Virus Capsids with Host Cell Polo-Like Kinases Are Important for Efficient Viral DNA Integration

Unlike for other retroviruses, only a few host cell factors that aid the replication of foamy viruses (FVs) via interaction with viral structural components are known. Using a yeast-two-hybrid (Y2H) screen with prototype FV (PFV) Gag protein as bait we identified human polo-like kinase 2 (hPLK2), a member of cell cycle regulatory kinases, as a new interactor of PFV capsids. Further Y2H studies confirmed interaction of PFV Gag with several PLKs of both human and rat origin. A consensus Ser-Thr/Ser-Pro (S-T/S-P) motif in Gag, which is conserved among primate FVs and phosphorylated in PFV virions, was essential for recognition by PLKs. In the case of rat PLK2, functional kinase and polo-box domains were required for interaction with PFV Gag. Fluorescently-tagged PFV Gag, through its chromatin tethering function, selectively relocalized ectopically expressed eGFP-tagged PLK proteins to mitotic chromosomes in a Gag STP motif-dependent manner, confirming a specific and dominant nature of the Gag-PLK interaction in mammalian cells. The functional relevance of the Gag-PLK interaction was examined in the context of replication-competent FVs and single-round PFV vectors. Although STP motif mutated viruses displayed wild type (wt) particle release, RNA packaging and intra-particle reverse transcription, their replication capacity was decreased 3-fold in single-cycle infections, and up to 20-fold in spreading infections over an extended time period. Strikingly similar defects were observed when cells infected with single-round wt Gag PFV vectors were treated with a pan PLK inhibitor. Analysis of entry kinetics of the mutant viruses indicated a post-fusion defect resulting in delayed and reduced integration, which was accompanied with an enhanced preference to integrate into heterochromatin. We conclude that interaction between PFV Gag and cellular PLK proteins is important for early replication steps of PFV within host cells.
Changes in platelet monoamine oxidase activity during abstinence.

Svaa,i¾. Platelet monoamine oxidase (MA O) activity in alcoholics increased transiently, without a corresponding increase in platelet counts, Jollowing cessation oJ drinking. Monoamine oxidase (aAO) is an enzyme responsible in part for the degradation of both catecholamines and indoleamines (1-3), neurotrans- mitters shown to influence behavior in animals (4-6) and implicated in a number of psychopathological conditions in humans (7). Because MAO is present in blood platelets and thus is easily accessible for measurement in clinical populations, it has been intensively investigated over the last decade. Reduced platelet MAO activity has been reported in bipolar affec- tive illness (8) and in schizophrenia (9), particularly chronic schizophre- nia. Secondary causes of lowAO activity (such as dietary deficiencies, medications, or other state-dependent variables) are thought not to ac- count for these findings, and longitudinal studies (e.g., 10) have generally demonstrated a fairly high degree of stability of plateletAO activity over time, irrespective of clinical state. In addition, studies of twins (9-12) have shown plateletAO to be predominantly under genetic control. The stability and heritability of plateletaAO have led investigators (11, 13) to suggest that low MAO activity might represent a genetic vulnerability factor for psychopathology. This hypothesis has been supported by a study (13) of normal populations in which there was a direct association be- tween lowAO and increased psychopathology, as well as an increased incidence of psychopathology in the families of those individuals with low MAO.
All-trans-retinoic acid inhibits chondrogenesis of rat embryo hindlimb bud mesenchymal cells by downregulating p53 expression

Despite the well-established role of all-trans-retinoic acid (ATRA) in congenital clubfoot (CCF)-like deformities in in vivo models, the essential cellular and molecular targets and the signaling mechanisms for ATRA-induced CCF-like deformities remain to be elucidated. Recent studies have demonstrated that p53 and p21, expressed in the hindlimb bud mesenchyme, regulate cellular proliferation and differentiation, contributing to a significant proportion of embryonic CCF-like abnormalities. The objective of the present study was to investigate the mechanisms for ATRA-induced CCF, by assessing ATRA-regulated chondrogenesis in rat embryo hindlimb bud mesenchymal cells (rEHBMCs) in vitro. The experimental study was based on varying concentrations of ATRA exposure on embryonic day 12.5 rEHBMCs in vitro. The present study demonstrated that ATRA inhibited the proliferation of cells by stimulating apoptotic cell death of rEHBMCs. It was also observed that ATRA induced a dose-dependent reduction of cartilage nodules compared with the control group. Reverse transcription-polymerase chain reaction and western blotting assays revealed that the mRNA and protein expression of cartilage-specific molecules, including aggrecan, Sox9 and collagen, type II, α 1 (Col2a1), were downregulated by ATRA in a dose-dependent manner; the mRNA levels of p53 and p21 were dose-dependently upregulated from 16 to 20 h of incubation with ATRA, but dose-dependently downregulated from 24 to 48 h. Of note, p53 and p21 were regulated at the translational level in parallel with the transcription with rEHBMCs treated with ATRA. Furthermore, the immunofluorescent microscopy assays indicated that proteins of p53 and p21 were predominantly expressed in the cartilage nodules. The present study demonstrated that ATRA decreases the chondrogenesis of rEHBMCs by inhibiting cartilage-specific molecules, including aggrecan, Sox9 and Col2al, via regulating the expression of p53 and p21.
Autonomous Cooperating Logistic Processes A Paradigm Shift and its Limitations CRC 637

This report describes several methods for reasoning with missing, irrelevant, and not applicable meta-values when learning concept descriptions or discovering patterns in data. The methods concern handling these values in datasets both for rule learning and for rule testing or application. The methods have been implemented in the AQ21 multitask learning and knowledge mining program, and experimentally tested on four datasets. The results illuminate relative strengths and limitations of the methods.
STUDY OF DIVERSITY INDICES AND ECOLOGICAL CHARACTERISTIC OF COASTALFLORA IN BHAL REGION (GUJARAT)

Gujarat is the state which has two gulfs in its 1600 km (approximately) area of coast out of 7517 km (approximately) coast line of India. Much work on diversity of mangroves and microbial diversity has been done in this area, but research on diversity of halophytes has not been much done. Attention was paid to listing, distribution and ecological aspects of plants growing in coastal areas. An attempt was made to study the diversity indices like Shannon’s index, Simpson index and Pielou’s index of coastal flora at 3 different habitats viz., marshy, fresh wetland and inland saline habitat during 3 seasons in Bhal region falling under Bhavnagar district (Gujarat). Results showed little variations for the indices for marshy locations (Sonrai Creek) during monsoon, winter and summer. In contrast, these measures of diversity marginally fluctuated at freshwater, saline and grassland localities.
Endocrine control of nutrient partition in lactating ruminants

subjects of nutrient partition during lactation in ruminants and the hormonal control of the relevant aspects of metabolism, in relation to blood hormone concentrations, of to describe the metabolic situation in lactating cows; to emphasize the more important aspects of the hormonal control of nutrient partition and to describe two of our recent experiments on the manipulation of hormone secretion.
A Major Haplotype Block at the Rho-Associated Kinase 2 Locus Is Associated with a Lower Risk of Hypertension in a Recessive Manner: The HYPGENE Study

The goals of our study were to evaluate the haplotype pattern at the Rho-associated kinase 2 (ROCK2) locus and prospectively test the association between the ROCK2 haplotype-tagging single-nucleotide polymorphisms (tagSNPs) with hypertension for verified incident hypertensive patients (n =607) and healthy, normotensive controls (n =586) in a HYPGENE study. Rho-associated kinases (ROCKs) play a central role in signaling pathways that are involved in vascular smooth muscle contraction and endothelial nitric oxide availability. Using a set of stringent criteria (minor allele frequency ≥0.05, pairwise r 2≥0.95), we identified 18 tagSNPs from the 109 SNPs available in the HapMap Caucasian data set. TagSNPs were genotyped using the Illumina BeadStation platform. The 18 tagSNPs consisted of two linkage disequilibrium (LD) blocks. A haplotype defined by four SNPs (rs965665, rs10178332, rs6755196, rs10929732) in LD block 2 was recessively associated with a lower risk of hypertension (p =0.003). Homozygotes for the minor alleles had an 85% lower risk of hypertension than carriers of the common allele. The associations were independent of baseline age, cardiorespiratory fitness, body mass index, sex, and follow-up time. The LD block 2 spans about 137 kb of genomic DNA at the 5'-end of the ROCK2 locus and covers exons encoding the kinase domain of the protein. Our data strongly suggest that a major haplotype block at the ROCK2 locus is recessively associated with a lower risk of hypertension. Identification of functional mutation(s) could thus help in the development of ROCK2-specific treatments.
Green love talks; cell–cell communication during double fertilization in flowering plants

A major breakthrough in understanding double fertilization has been made by high resolution live-imaging. This has helped resolve several disputed issues such as preferential fertilization and polyspermy block. Cumulated information of molecular components involved in double fertilization highlights the importance of cell-cell communication between male and female gametophytes.
US2StarTool: Generating i* Models From User Stories

In agile methods, the requirements are represented by user stories. However, this model does not allow a good visualization of context in which a story is inserted, reducing the understanding of the system as a whole. On the other hand, the i* model presents dependencies among organizational actors, and the understanding of the context in which a requirement is inserted. This paper presents an implementation of an automated solution as a tool to mapping user stories into i* models, US2StarTool, adding a support for agile develop- ment environment. US2StarTool can help requirements engineer in agile devel- opment environments contextualizing the environment in which user stories are inserted and showing relationships between the actors and the system.
Design of a biomimetic fish caudal drive via Macro Fiber Composite

According to the technology of the body-and-caudal fin drive, a novel design of biomimetic caudal drive is proposed in this paper. The drive is a two-layer laminated plate that is composed of Macro Fiber Composite (MFC) and a substrate of variable stiffness. When the material of the substrate is glass fiber epoxy reinforced composites, the biggest displacement of the terminal is 4mm in the air and 1.97mm under the water, and when the material is glass fiber composites of polyurethane, the biggest displacement is 2.39mm in the air. Therefore, the experiments verify the feasibility of the design and the significance of the substrate's stiffness for the drive of the caudal fin.
Mobile Payments Go Viral: M-PESA in Kenya

M-PESA is a small-value electronic payment and store of value system that is accessible from ordinary mobile phones. It has seen exceptional growth since its introduction by mobile phone operator Safaricom in Kenya in March 2007: it has already been adopted by 9 million customers (corresponding to 40 percent of Kenya's adult population) and processes more transactions domestically than Western Union does globally. M-PESA's market success can be interpreted as the interplay of three sets of factors: (i) pre-existing country conditions that made Kenya a conducive environment for a successful mobile money deployment; (ii) a clever service design that facilitated rapid adoption and early capturing of network effects; and (iii) a business execution strategy that helped M-PESA rapidly reach a critical mass of customers, thereby avoiding the adverse chicken-and-egg (two-sided market) problems that afflict new payment systems.
MELB-MKB: Lexical Substitution system based on Relatives in Context

In this paper we describe the MELB-MKB system, as entered in the SemEval-2007 lexical substitution task. The core of our system was the "Relatives in Context" unsupervised approach, which ranked the candidate substitutes by web-lookup of the word sequences built combining the target context and each substitute. Our system ranked third in the final evaluation, performing close to the top-ranked system.
Di-μ-methoxido-μ-oxido-bis[triphenylantimony(V)] methanol disolvate

The title compound, [Sb2(C6H5)6(CH3O)2O]·2CH3OH, is the methanol disolvate of a dinuclear triphenylantimony derivative. The molecule shows C s symmetry. The Sb—O—Sb angles cover a range from 89.65 (10)° to 102.08 (13)°. In the crystal structure, two O—H⋯O hydrogen bonds are present.
Hypothesis Testing based Intrinsic Evaluation of Word Embeddings

We introduce the cross-match test - an exact, distribution free, high-dimensional hypothesis test as an intrinsic evaluation metric for word embeddings. We show that cross-match is an effective means of measuring the distributional similarity between different vector representations and of evaluating the statistical significance of different vector embedding models. Additionally, we find that cross-match can be used to provide a quantitative measure of linguistic similarity for selecting bridge languages for machine translation. We demonstrate that the results of the hypothesis test align with our expectations and note that the framework of two sample hypothesis testing is not limited to word embeddings and can be extended to all vector representations.
Towards Privacy-Preserving XML Transformation

In composite web services one can only either hide the identities of the participants or provide end-to-end confidentiality via encryption. For a designer of inter-organizational business processes this implies that she either needs to reveal her suppliers or force her customers to reveal their information. In this paper we present a solution to the encrypted data modification problem and recon ciliate this apparent conflict. Using a generic sender-transformer-recipient example scenario, we illustrate the steps required for applying XML transformations to encrypted data, present the cryptographic building blocks, and give an outlook on advantages and weaknesses of the proposed encryption scheme. The transformer is then able to offer composite services without itself learning the content of the messages.
Image quality and entropy masking

Image quality models usually include a mechanism whereby artifacts are masked by the image acting as a background. Scientific study of visual masking has followed two traditions: contrast masking and noise masking, depending primarily on whether the mask is deterministic or random. In the former tradition, masking is explained by a decrease in the effective gain of the early visual system. In the latter tradition, masking is explained by an increased variance in some internal decision variable. The masking process in image quality models is usually of the gain-control variety, derived from the contrast masking tradition. In this paper we describe a third type of masking, which I call entropy masking, that arises when the mask is deterministic but unfamiliar. Some properties and implication of entropy masking are discussed. We argue that image quality models should incorporate entropy masking, as well as contrast masking.
CDC-42 and RHO-1 coordinate acto-myosin contractility and PAR protein localization during polarity establishment in C. elegans embryos

In C. elegans one-cell embryos, polarity is conventionally defined along the anteroposterior axis by the segregation of partitioning-defective (PAR) proteins into anterior (PAR-3, PAR-6) and posterior (PAR-1, PAR-2) cortical domains. The establishment of PAR asymmetry is coupled with acto-myosin cytoskeleton rearrangements. The small GTPases RHO-1 and CDC-42 are key players in cytoskeletal remodeling and cell polarity in a number of different systems. We investigated the roles of these two GTPases and the RhoGEF ECT-2 in polarity establishment in C. elegans embryos. We show that CDC-42 is required to remove PAR-2 from the cortex at the end of meiosis and to localize PAR-6 to the cortex. By contrast, RHO-1 activity is required to facilitate the segregation of CDC-42 and PAR-6 to the anterior. Loss of RHO-1 activity causes defects in the early organization of the myosin cytoskeleton but does not inhibit segregation of myosin to the anterior. We therefore propose that RHO-1 couples the polarization of the acto-myosin cytoskeleton with the proper segregation of CDC-42, which, in turn, localizes PAR-6 to the anterior cortex.