Miracle-dz/UniFAR-FTUs huggingface dataset:
Active + Semi-supervised Learning = Robust Multi-View Learning

In a multi-view problem, the features of the domain can be partitioned into disjoint subsets (views) that are sufficient to learn the target concept. Semi-supervised, multi-view algorithms, which reduce the amount of labeled data required for learning, rely on the assumptions that the views are compatible and uncorrelated (i.e., every example is identically labeled by the target concepts in each view; and, given the label of any example, its descriptions in each view are independent). As these assumptions are unlikely to hold in practice, it is crucial to understand the behavior of multi-view algorithms on problems with incompatible, correlated views. We address this issue by studying several algorithms on a parameterized family of text classification problems in which we control both view correlation and incompatibility. We first show that existing semi-supervised algorithms are not robust over the whole spectrum of parameterized problems. Then we introduce a new multi-view algorithm, Co-EMT, which combines semi-supervised and active learning. Co-EMT outperforms the other algorithms both on the parameterized problems and on two additional real world domains. Our experiments suggest that Co-EMT’s robustness comes from active learning compensating for the correlation of the views.
Toward Deep Learning Software Repositories

Deep learning subsumes algorithms that automatically learn compositional representations. The ability of these models to generalize well has ushered in tremendous advances in many fields such as natural language processing (NLP). Recent research in the software engineering (SE) community has demonstrated the usefulness of applying NLP techniques to software corpora. Hence, we motivate deep learning for software language modeling, highlighting fundamental differences between state-of-the-practice software language models and connectionist models. Our deep learning models are applicable to source code files (since they only require lexically analyzed source code written in any programming language) and other types of artifacts. We show how a particular deep learning model can remember its state to effectively model sequential data, e.g., Streaming software tokens, and the state is shown to be much more expressive than discrete tokens in a prefix. Then we instantiate deep learning models and show that deep learning induces high-quality models compared to n-grams and cache-based n-grams on a corpus of Java projects. We experiment with two of the models' hyper parameters, which govern their capacity and the amount of context they use to inform predictions, before building several committees of software language models to aid generalization. Then we apply the deep learning models to code suggestion and demonstrate their effectiveness at a real SE task compared to state-of-the-practice models. Finally, we propose avenues for future work, where deep learning can be brought to bear to support model-based testing, improve software lexicons, and conceptualize software artifacts. Thus, our work serves as the first step toward deep learning software repositories.
Testosterone increases activity but not daily energy expenditure in captive male dark-eyed juncos, Junco hyemalis


Plasma testosterone (T) levels in male dark-eyed juncos peak early in the breeding season, then decline. If T enhances opportunities for reproductive success, as suggested by previous experiments, why does elevated T not occur naturally? To address this question, we prolonged the early peak level throughout the breeding season and explored potential energetic costs of maintaining elevated T. We measured daily energy expenditure (DEE) of treated males (T-males) and controls (C-males) using doubly labelled water (DLW). We also conducted behaviour scans of T- and C-males housed in outdoor aviaries. DEE was not higher in T-males than in C-males. However, T-males did increase locomotion and foraging and decrease rest and self-maintenance. These results suggest that elevated T may increase the contribution of some components of DEE and lower the contribution of others. Furthermore, the T-induced decrease in allocation of time to rest and maintenance may represent a long-term cost that has led to selection against the maintenance of elevated T beyond the natural early spring peak. Copyright 2000 The Association for the Study of Animal Behaviour.
S phase block following MEC1ATR inactivation occurs without severe dNTP depletion

ABSTRACT Inactivation of Mec1, the budding yeast ATR, results in a permanent S phase arrest followed by chromosome breakage and cell death during G2/M. The S phase arrest is proposed to stem from a defect in Mec1-mediated degradation of Sml1, a conserved inhibitor of ribonucleotide reductase (RNR), causing a severe depletion in cellular dNTP pools. Here, the casual link between the S phase arrest, Sml1, and dNTP-levels is examined using a temperature sensitive mec1 mutant. In addition to S phase arrest, thermal inactivation of Mec1 leads to constitutively high levels of Sml1 and an S phase arrest. Expression of a novel suppressor, GIS2, a conserved mRNA binding zinc finger protein, rescues the arrest without down-regulating Sml1 levels. The dNTP pool in mec1 is reduced by ∼17% and GIS2 expression restores it, but only partially, to ∼93% of a control. We infer that the permanent S phase block following Mec1 inactivation can be uncoupled from its role in Sml1 down-regulation. Furthermore, unexpectedly modest effects of mec1 and GIS2 on dNTP levels suggest that the S phase arrest is unlikely to result from a severe depletion of dNTP pool as assumed, but a heightened sensitivity to small changes in its availability. Summary: This study, using a temperature sensitive mec1 mutant, reveals that inactivation of Mec1 leads to S phase arrest, and that genome duplication in the absence of Mec1/ATR is exquisitely sensitive to small changes in dNTP levels.
Tracing Lineage Beyond Relational Operators

Tracing the lineage of data is an important requirement for establishing the quality and validity of data. Recently, the problem of data provenance has been increasingly addressed in database research. Earlier work has been limited to the lineage of data as it is manipulated using relational operations within an RDBMS. While this captures a very important aspect of scientific data processing, the existing work is incapable of handling the equally important, and prevalent, cases where the data is processed by non-relational operations. This is particularly common in scientific data where sophisticated processing is achieved by programs that are not part of a DBMS. The problem of tracking lineage when non-relational operators are used to process the data is particularly challenging since there is potentially no constraint on the nature of the processing. In this paper we propose a novel technique that overcomes this significant barrier and enables the tracing of lineage of data generated by an arbitrary function. Our technique works directly with the executable code of the function and does not require any high-level description of the function or even the source code. We establish the feasibility of our approach on a typical application and demonstrate that the technique is able to discern the correct lineage. Furthermore, it is shown that the method can help identify limitations in the function itself.
Recognition of pathogen-associated nucleic acids by endosomal nucleic acid-sensing toll-like receptors

Abstract Foreign nucleic acids, the essential signature molecules of invading pathogens that act as danger signals for host cells, are detected by endosomal nucleic acid-sensing toll-like receptors (TLRs) 3, 7, 8, 9, and 13. These TLRs have evolved to recognize ‘non-self’ nucleic acids within endosomal compartments and rapidly initiate innate immune responses to ensure host protection through induction of type I interferons, inflammatory cytokines, chemokines, and co-stimulatory molecules and maturation of immune cells. In this review, we highlight our understanding of the recognition of pathogen-associated nucleic acids and activation of corresponding signaling pathways through endosomal nucleic acid-sensing TLRs 3, 7, 8, 9, and 13 for an enormous diversity of pathogens, with particular emphasis on their compartmentalization, intracellular trafficking, proteolytic cleavage, autophagy, and regulatory programs.
Conversation and Compliance: Role of Interpersonal Discussion and Social Norms in Public Communication Campaigns

This study explores the role of interpersonal discussion and social norms in a public health campaign, the BBC Condom Normalization Campaign, designed to promote conversation and change the public perception of condom use in India. Drawing upon the integrative model of behavioral prediction, attitudes, self-efficacy, subjective norms, and descriptive norms were predicted to relate to behavioral intentions to use condoms. It is important to note that the valence of discussion was hypothesized to relate to each of these more proximal predictors. The authors used structural equation modeling to test the model on 3 separate samples of Indian men between the ages of 15 and 49 years: (a) high-risk men who had sex with nonspouses; (b) low-risk, sexually inactive, unmarried men; and (c) low-risk, monogamous, married men. Results were similar for low- and high-risk audiences, with valence of discussion about condoms predicting condom-related attitudes, self-efficacy, and subjective and descriptive social norms with respect to condom use, which, in turn, predicted behavioral intent to use condoms. These findings underscore the need to take not only the frequency but also the valence of interpersonal discussion into account when assessing the effect of health campaigns. Implications for theory and design of future public communication campaigns are explored.
Insights into mantle structure and flow beneath Alaska based on a decade of observations of shear wave splitting

SKS shear wave splitting measurements from three Program for Array Seismic Studies of the Continental Lithosphere experiments (Broadband Experiment Across the Alaska Range, Alaska Receiving Cross Transect of the Inner Core, and Multidisciplinary Observations Of Subduction), which form a north/south transect across Alaska, show a remarkably simple pattern of two large anisotropy domains. In the northern domain, extending from the 70 km contour of the subducting Pacific plate north to the Arctic Ocean, fast directions are consistently in the NE‐SW direction. These directions are essentially parallel to the absolute plate motion direction in northern Alaska and parallel to the strike of the subducting plate above the mantle wedge, suggesting that they represent some combination of plate‐scale asthenospheric flow in the upper mantle and flow along the subducting plate in the mantle wedge. A strong wedge component beneath the Alaska Range is required to explain systematics of splitting delay times. In the southern domain, which extends south from the 70 km depth contour to the subducting plate, fast directions are in the NW‐SE direction, a 90° rotation from the northern domain. These fast directions are parallel to the dip of the subducting plate in the direction of convergence and represent entrained flow beneath the subducting slab; the Pacific Plate absolute motion approximately parallels local convergence. Two major factors seem to control flow in these regions, absolute plate motion in the north and the subduction of the Pacific plate in the south, although both subduction‐driven wedge flow and absolute plate motion contribute to the southern part of the northern regime.
A controlled trial of antidepressants in patients with Parkinson disease and depression

Background: Parkinson disease (PD) is a common neurodegenerative disease affecting up to 1 million individuals in the United States. Depression affects up to 50% of these patients and is associated with a variety of poor outcomes for patients and their families. Despite this, there are few evidence-based data to guide clinical care. Methods: An NIH-funded, randomized, controlled trial of paroxetine CR, nortriptyline, and placebo in 52 patients with PD and depression. The primary outcomes were the change in the Hamilton Depression Rating Scale (HAM-D) and the percentage of depression responders at 8 weeks. Results: Nortriptyline was superior to placebo for the change in HAM-D (p < 0.002); paroxetine CR was not. There was a trend for superiority of nortriptyline over paroxetine CR at 8 weeks (p < 0.079). Response rates favored nortriptyline (p = 0.024): nortriptyline 53%, paroxetine CR 11%, placebo 24%. In planned contrasts of response rates, nortriptyline was superior to paroxetine CR (p = 0.034). Nortriptyline was also superior to placebo in many of the secondary outcomes, including sleep, anxiety, and social functioning, while paroxetine CR was not. Both active drug treatments were well tolerated. Conclusions: Though relatively modest in size, this is the largest placebo-controlled trial done to date in patients with Parkinson disease (PD) and depression. Nortriptyline was efficacious in the treatment of depression and paroxetine CR was not. When compared directly, nortriptyline produced significantly more responders than did paroxetine CR. The trial suggests that depression in patients with PD is responsive to treatment and raises questions about the relative efficacy of dual reuptake inhibitors and selective serotonin reuptake inhibitors. ARR = absolute risk reduction; DSM-IV = Diagnostic and Statistical Manual of Mental Disorders, 4th edition; HAM-A = Hamilton Anxiety Scale; HAM-D = Hamilton Depression Rating Scale; MMSE = Mini-Mental State Examination; NNT = number needed to treat; PD = Parkinson disease; PDQ = Parkinson’s Disease Questionnaire; PSQI = Pittsburgh Sleep Quality Index; SCID = Structured Clinical Interview; SSRI = selective serotonin reuptake inhibitor; TCA = tricyclic antidepressant; UPDRS = Unified Parkinson’s Disease Rating Scale.
Mapping of three porcine 20S proteasome genes using the IMpRH panel

The 26S proteasome is a multicatalytic enzyme complex that plays a central role in all regulatory pathways such as cell cycle regulation, differentiation, and apoptosis. The 26S proteasome has three components, 20S proteasome, PA28 (Proteasome Activator 28) and PA700 (Proteasome Activator 700) subunits. The combination of PA28 and 20S proteasomes greatly increases the proteasome-mediated proteolysis activity, which is important in the processing and presentation of some antigens. The three genes related to PA28 and seven genes related to PA700 have been mapped by our group (Wang et al., 2003, 2004; Yu et al., 2004). Here we report our mapping results on the PSMA5, PSMB3 and PSMB6 genes, which were thought to be part of the 20S proteasome, the core of the 26S proteasome. Materials and methods
Agrobacterium-mediated transformation of durum wheat (Triticum turgidum L. var. durum cv Stewart) with improved efficiency

An efficient Agrobacterium-mediated durum wheat transformation system has been developed for the production of 121 independent transgenic lines. This improved system used Agrobacterium strain AGL1 containing the superbinary pGreen/pSoup vector system and durum wheat cv Stewart as the recipient plant. Acetosyringone at 400 μM was added to both the inoculation and cultivation medium, and picloram at 10 mg l−1 and 2 mg l−1 was used in the cultivation and induction medium, respectively. Compared with 200 μM in the inoculation and cultivation media, the increased acetosyringone concentration led to significantly higher GUS (β-glucuronidase) transient expression and T-DNA delivery efficiency. However, no evident effects of acetosyringone concentration on regeneration frequency were observed. The higher acetosyringone concentration led to an improvement in average final transformation efficiency from 4.7% to 6.3%. Furthermore, the concentration of picloram in the co-cultivation medium had significant effects on callus induction and regeneration. Compared with 2 mg l−1 picloram in the co-cultivation medium, increasing the concentration to 10 mg l−1 picloram resulted in improved final transformation frequency from 2.8% to 6.3%, with the highest frequency of 12.3% reached in one particular experiment, although statistical analysis showed that this difference in final transformation efficiency had a low level of significance. Stable integration of foreign genes, their expression, and inheritance were confirmed by Southern blot analyses, GUS assay, and genetic analysis. Analysis of T1 progeny showed that, of the 31 transgenic lines randomly selected, nearly one-third had a segregation ratio of 3:1, while the remainder had ratios typical of two or three independently segregating loci.
A Model of Tuberculosis Screening for Pregnant Women in Resource-Limited Settings Using Xpert MTB/RIF

Timely diagnosis and treatment of maternal tuberculosis (TB) is important to reduce morbidity and mortality for both the mother and child, particularly in women who are coinfected with HIV. The World Health Organization (WHO) recommends the integration of TB/HIV screening into antenatal services but available diagnostic tools are slow and insensitive, resulting in delays in treatment initiation. Recently the WHO endorsed Xpert MTB/RIF, a highly sensitive, real-time PCR assay for Mycobacterium tuberculosis that simultaneously detects rifampicin resistance directly from sputum and provides results within 100 minutes. We propose a model for same-day TB screening and diagnosis of all pregnant women at antenatal care using Xpert MTB/RIF. Pilot studies are urgently required to evaluate strategies for the integration of TB screening into antenatal clinics using new diagnostic technologies.
Click and Mortar Strategies Viewed from the Web: A Content Analysis of Features Illustrating Integration Between Retailers' Online and Offline Presence

E‐commerce researchers have shown that retailers are increasingly following a click and mortar strategy, whereby online and offline channels are becoming more integrated. Despite case study evidence for the benefit of this approach, an analysis of the websites of nearly 1,000 US‐based retailers having both an online and offline presence reveals that a high degree of integration across channels is relatively uncommon. On the contrary, the study reported here demonstrates that retailers are more likely to pursue easy‐to‐accomplish, low intensity, informational integration when developing an online presence, exemplified by such features as a listing of store locations or hours. Few retail websites offer complex integration capabilities, such as the ability to search local store inventories, or to pick up and return online purchases in a local outlet. Regression analyses reveal that the retail sector and firm resources help to explain this discrepancy. With regard to sector, some product types require more ph.
The Porcine MicroRNA Transcriptome Response to Transmissible Gastroenteritis Virus Infection

Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases.
Serological and Virological Characterization of Clinically Diagnosed Cases of Measles in Suburban Khartoum

ABSTRACT Measles continues to be a major childhood disease in terms of global morbidity and mortality. In the main areas of its endemicity the only available means of diagnosis are based on clinical criteria: the presence of a maculopapular rash and fever accompanied by cough, coryza, and/or conjunctivitis. We have studied 38 clinically diagnosed cases of measles in Khartoum, Sudan, by means of serology, reverse transcriptase PCR (RT-PCR) on throat swabs and virus isolation from lymphocytes. On the basis of serology, 28 patients were diagnosed as having an acute measles virus (MV) infection, while in 10 cases the clinical symptoms proved to have other causes. It was shown that in cases with low serum immunoglobulin M (IgM) levels, an additional measurement of IgG or virus-neutralizing antibodies was necessary to discriminate between patients with an acute MV infection sampled during an early stage of the disease and patients who had experienced an MV infection in the more distant past. The serological laboratory diagnosis was validated by an MV-specific RT-PCR: for all confirmed measles cases tested a fragment of the correct size which hybridized with a third MV-specific primer could be amplified, while all serologically negative cases were also RT-PCR negative. MV could be isolated from 17 out of 23 of the serologically confirmed cases, demonstrating that virus isolation is less reliable as a diagnostic tool than serology or RT-PCR. This study stresses the urgent need for a rapid diagnostic field test for measles.
Competitive Nonlinear Taxation and Constitutional Choice

In an economy where agents have different productivities and mobility, we compare a unified nonlinear optimal taxation with the equilibrium taxation that would be chosen by two competing tax authorities if the same economy were divided into two states. The overall level of progressivity and redistribution is unambiguously lower under competitive taxation; the "rich" are always in favor of competing authorities, whereas the "poor" are always in favor of unified taxation; the preferences of the middle class depend on the initial conditions in terms of the distribution of abilities, the relative power of the various classes, and mobility costs. (JEL D72, H21, H23, H24)
Expansion of Dust Provenance and Aridification of Asia Since ~7.2 Ma Revealed by Detrital Zircon U‐Pb Dating

The relative importance of global cooling and Tibetan Plateau uplift in driving the aridification of Asia during the late Cenozoic is debated, largely due to the lack of appropriate proxy indicators. Here we address this problem by investigating changes in the source of Chinese loess and Red Clay, which is directly controlled by changes in the extent and distribution of the arid zone of Asia and the intensity of the East Asian winter monsoon, using zircon U‐Pb dating of 27 levels in a near‐continuous eolian sedimentary sequence in southern Chinese Loess Plateau. The results show that source regions expanded stepwise at ~7.2, ~2.6, 1.2–0.9 Ma, and at the Last Glacial Maximum. These changes were synchronous with global cooling and ice cover expansion in the Northern Hemisphere, suggesting that the drivers of aridification of the Asian interior were intimately related to global cooling in the late Cenozoic.