Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-Müllerian Hormone Concentrations in Premenopausal Women and Breast Cancer Risk

Laboratory models support an inverse association between anti-Müllerian hormone (AMH) and breast tumor development. Human studies are lacking; one study (N = 105 cases, 204 controls) with prospectively collected serum reported the opposite—an approximate 10-fold increase in breast cancer risk comparing fourth with first quartile AMH levels. We investigated the relation between serum AMH levels and breast cancer risk in a case–control (N = 452 cases, 902 controls) study nested within the prospective Sister Study cohort of 50,884 women. At enrollment, participants were ages 35 to 54, premenopausal, and completed questionnaires on medical and family history, lifestyle factors, and demographics. AMH (ng/mL) was measured by ultrasensitive ELISA in serum collected at enrollment and log-transformed for analysis. Multivariate conditional logistic regression was used to calculate ORs and 95% confidence intervals (CI) to account for matching on age and enrollment year. Mean age at enrollment was 46.8 years with an average 2.9 years from blood draw to breast cancer diagnosis (SD = 1.9). AMH concentrations were below the limit of detection (0.003 ng/mL) for approximately 25% of samples. Compared with samples below the LOD, women with AMH >2.84 ng/mL (90th percentile among controls) had a 2-fold increase in breast cancer odds (OR, 2.25; 95% CI, 1.26–4.02). For each 1-unit increase in lnAMH, overall breast cancer odds increased by 8% (OR, 1.08; 95% CI, 1.02–1.15) and odds of estrogen receptor–positive, invasive disease increased by 15% (OR, 1.15; 95% CI, 1.05–1.25). Our findings demonstrate an overall positive relation between AMH and breast cancer. Cancer Prev Res; 8(6); 528–34. ©2015 AACR.
Inference of transcriptional regulation in cancers

Significance We developed an efficient and accurate computational framework, RABIT (regression analysis with background integration), and comprehensively integrated public transcription factor (TF)-binding profiles with TCGA tumor-profiling datasets in 18 cancer types. To systematically search for cancer-associated TFs, RABIT controls the effect of tumor-confounding factors on transcriptional regulation, such as copy number alteration, DNA methylation, and TF somatic mutation. Our predicted TF regulatory activity in tumors is highly consistent with the knowledge from cancer gene databases and reveals many previously unidentified cancer-associated TFs. We also analyzed RNA-binding protein regulation in cancer and demonstrated that RABIT is a general platform for predicting oncogenic gene expression regulators. Despite the rapid accumulation of tumor-profiling data and transcription factor (TF) ChIP-seq profiles, efforts integrating TF binding with the tumor-profiling data to understand how TFs regulate tumor gene expression are still limited. To systematically search for cancer-associated TFs, we comprehensively integrated 686 ENCODE ChIP-seq profiles representing 150 TFs with 7484 TCGA tumor data in 18 cancer types. For efficient and accurate inference on gene regulatory rules across a large number and variety of datasets, we developed an algorithm, RABIT (regression analysis with background integration). In each tumor sample, RABIT tests whether the TF target genes from ChIP-seq show strong differential regulation after controlling for background effect from copy number alteration and DNA methylation. When multiple ChIP-seq profiles are available for a TF, RABIT prioritizes the most relevant ChIP-seq profile in each tumor. In each cancer type, RABIT further tests whether the TF expression and somatic mutation variations are correlated with differential expression patterns of its target genes across tumors. Our predicted TF impact on tumor gene expression is highly consistent with the knowledge from cancer-related gene databases and reveals many previously unidentified aspects of transcriptional regulation in tumor progression. We also applied RABIT on RNA-binding protein motifs and found that some alternative splicing factors could affect tumor-specific gene expression by binding to target gene 3′UTR regions. Thus, RABIT (rabit.dfci.harvard.edu) is a general platform for predicting the oncogenic role of gene expression regulators.
Variable Threshold of Trigeminal Cold-Thermosensitive Neurons Is Determined by a Balance between TRPM8 and Kv1 Potassium Channels

Molecular determinants of threshold differences among cold thermoreceptors are unknown. Here we show that such differences correlate with the relative expression of I KD, a current dependent on Shaker-like Kv1 channels that acts as an excitability brake, and I TRPM8, a cold-activated excitatory current. Neurons responding to small temperature changes have high functional expression of TRPM8 (transient receptor potential cation channel, subfamily M, member 8) and low expression of I KD. In contrast, neurons activated by lower temperatures have a lower expression of TRPM8 and a prominent I KD. Otherwise, both subpopulations have nearly identical membrane and firing properties, suggesting that they belong to the same neuronal pool. Blockade of I KD shifts the threshold of cold-sensitive neurons to higher temperatures and augments cold-evoked nocifensive responses in mice. Similar behavioral effects of I KD blockade were observed in TRPA1−/− mice. Moreover, only a small percentage of trigeminal cold-sensitive neurons were activated by TRPA1 agonists, suggesting that TRPA1 does not play a major role in the detection of low temperatures by uninjured somatic cold-specific thermosensory neurons under physiological conditions. Collectively, these findings suggest that innocuous cooling sensations and cold discomfort are signaled by specific low- and high-threshold cold thermoreceptor neurons, differing primarily in their relative expression of two ion channels having antagonistic effects on neuronal excitability. Thus, although TRPM8 appears to function as a critical cold sensor in the majority of peripheral sensory neurons, the expression of Kv1 channels in the same terminals seem to play an important role in the peripheral gating of cold-evoked discomfort and pain.
Literacy discussions in low-income families: The effect of parent questions on fourth graders’ retellings

This study examines the effects of four types of reading comprehension questions – immediate, non-immediate, summary, and unanswerable questions – that linguistically diverse and predominantly low-income parents asked their fourth graders on children’s text retellings. One-hundred-twenty (N = 120) parent and child dyads participated in a home visit study in which they talked about narrative and informational texts. Moderation analyses indicated that immediate questions and non-immediate questions had a more positive effect on student retellings of an informational text and a narrative text, respectively, for less proficient than more proficient readers. These findings suggest that parents may be able to help their children, particularly less proficient readers, with text memory and text comprehension by asking specific types of questions.
From pest to partner: rethinking the Australian White Ibis in the more-than-human city

Calls to rethink our ethical and political responsibilities with nonhuman others abound recent work in cultural geography. Such work unpacks the more-than-human agencies reshaping and rematerialising our bodies and subjective knowledges. This article uncovers the coproduction of human knowledges and urban spaces by examining the problematic migration of the Australian White Ibis into Australian urban localities. We put forth a storied approach to human-ibis relations, capturing the multiple and situated experiences materialising our urban relations with the species. Drawing on ibis ethology, media narratives, personal and interviewee stories, we explore how ibis take part in the co-constitution of urban spaces and identities. In particular, we examine how the ibis as a pest narrative is mobilised and reproduced in public and media discourses that shape the species identity and influence modes of relating. Both the publics and our own personal intra-actions with ibis shed light on conceptions of nonhuman belonging, death and human desires for living-with. This article forwards a cosmopolitical approach to provoke a reconceptualisation of our ethical and political responsibility with urban ibis. We question the narrative of ibis-as-pest to forward ideas of living-with that provokes new modes of relating, uncomfortable for either party. Within these precarious relations, possibilities open for nonhierarchical modes of cohabitation, challenging our political and ethical responsibilities in living-with uncomfortable others.
Nonlinear analysis of the Lorenz system and buck converter using GPU

In this paper, we present the bifurcation analysis and the atraction basins of two systems using brute force algorithms executed in parallel way on GPU. The algorithms were developed in C language and using CUDA libraries for the parallel programming. The first system to be analyzed is the Lorenz system. This smooth nonlinear system has been studied using GPU. The second one is a piecewise smooth system, this is the buck converter controlled by sine wave. There are not studies in the literature about nonlinear analysis of this system using GPU. Numerical experiments were performed in parallel way on two GPUs and sequentially on a CPU. We achieve speed ups near to 102X. Finally, we present some comparisons of execution times on different architectures.
Virophage control of antarctic algal host–virus dynamics

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator–prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25–100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host–virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.
Gender and the Japanese State: Pension Benefits Creating Difference

This article analyzes the Japanese public pension system for classifications and valuations by gender, class, and age. In modern states government policies provide subject positions for people as citizens and workers that constitute them in certain identities and relationships. Japanese pension policies offer a pattern of subject positions that reproduces the high economic growth underlying the power of the Japanese state. Government pensions support government employees and employees of large and medium companies along with their dependent wives far better than the self-employed in small businesses and agriculture whose wives are assumed to be independently working. In the 1986 reforms women received contradictory subject positions as government policies encouraged them on one hand to be continual full-time workers and on the other to be dependent wives of salaried men, who work part-time without pension benefits. [Japan, pension, welfare, class, gender]
International Journal of Pure and Applied Sciences and Technology Biosorption of Heavy Metals from Aqueous Solution Using Bacillus Licheniformis

Current problems of heavy metal pollution in urban and rural ground water resources as well as sea water are reducing the potability of drinking water. Besides, there are several ill effects on human/animal health due to toxicity of heavy metals in soil and water. Conventionally physiochemical methods are used for the removal of metals. However, considering their limitations and certain disadvantages, biological methods mainly biosorption are preferred. In this work we have used living biomass of Bacillus licheniformis, which is already employed in sewage treatment. Aerobic batch biosorption experiments were carried out for removal of Cr (VI), Fe (III), Cu (II) ions from aqueous metal solutions. % removal efficiency for iron, chromium and copper ions was 95, 52 and 32 (w/v) after 48 hrs at 120 rpm. Optimum pH was found to be 3.5 for Fe (III) and Cr (VI) whereas for Cu (II) it was 2.5. Optimum incubation temperature was found to be 28 ºC. Metal tolerance studies were also carried out using aqueous metal solutions of these metals individually and in combination. The maximum tolerable concentration was 1200 mg L-1 for Cr (VI) while it was above 1500 mg L-1 for Fe (III) and Cu (II). MTC for the set having combination of all metals in equal amount was 1000 mg L-1. Interestingly the organism was found to tolerate upto 1000 mg L-1 concentration of heavy metals when a mixture of them (each at equal concentration) was used. Our study is an attempt to provide a multipurpose alternative for waste water treatment.
Islet transplantation for diabetes: current status and future prospects

There has been an explosion of interest in developing transplantation strategies to replace the islets lost during the normal progression of diabetes. In large part, the renewed interest is due to the unprecedented success of the ‘Edmonton protocol’ for Type I diabetics following islet allografting and a modified immunosuppressive regimen. While these data provide a clear and unequivocal demonstration that islet transplantation is a viable treatment strategy, the shortage of suitable donor tissue, together with the debilitating consequences of life long immunosuppression necessitate a concerted effort to develop novel means to enable islet transplantation on a widespread basis. This review outlines several of these possibilities including the development of novel, less toxic immunosuppressants, tolerising the host immune system to accept islet transplants, developing alternative sources of islet cells via gene therapy, stem cell technologies and xenotransplantation, immunoisolation of islets and providing local immunosuppression to islet grafts using Sertoli cells. These possibilities are highlighted in the context of islet cell transplantation as a success, but with need for further refinements before it is a panacea for most patients.
Bringing computer science back into schools: lessons from the UK

Computer science in UK schools is a subject in decline: the ratio of Computing to Maths A-Level students (i.e. ages 16--18) has fallen from 1:2 in 2003 to 1:20 in 2011 and in 2012. In 2011 and again in 2012, the ratio for female students was 1:100, with less than 300 female students taking Computing A-Level in the whole of the UK each year. Similar problems have been observed in the USA and other countries, despite the increased need for computer science skills caused by IT growth in industry and society. In the UK, the Computing At School (CAS) group was formed to try to improve the state of computer science in schools. Using a combination of grassroots teacher activities and policy lobbying at a national level, CAS has been able to rapidly gain traction in the fight for computer science in schools. We examine the reasons for this success, the challenges and dangers that lie ahead, and suggest how the experience of CAS in the UK can benefit other similar organisations, such as the CSTA in the USA.
Evaluating multiagent systems: a record/replay approach

The adoption of multiagent systems by companies and users requires that it is possible to verify the properties of the multiagent systems. The main candidate of this verification is model checking but as sketched in the paper, it presents drawbacks such as combinatorial explosion or it does not take the environment into account. Model checking seems to be restricted to small systems with few agents. We present a different approach used in testing called the record/replay mechanism. We add as well a post-mortem analysis. This work describes the advantages of this approach and how we have implemented it in the MadKit platform.
The EDM Vis Tool

We introduce EDM Vis, an information visualization software tool for exploring, navigating and understanding student datalogs. EDM Vis loads student logs, entire classes, hundreds of students, at a time, and displays the student behavior of thosestudents as they solved problems using a software tutor. The visualization uses a tree structure to provide an overview of classperformance, and interface elements to allow easy navigation and exploration of student behavior.
Effects of Different Tissue Adhesives in Treating Calvarial Bone Defects

Abstract The purpose of this study is to investigate the potential of the 2 different tissue adhesive materials as a barrier for guided bone regeneration and to compare them with resorbable collogen membrane on autogenous grafted critical-sized cortical bone defects. Twenty-four rats were divided into 3 groups: Group M, Group G, and Group B. A 5-mm diameter critical-size defect was created in the calvarium of each animal. All defects were filled by autogenous graft harvested from tibia. In group M, resorbable collogen membrane was applied to defect area. In groups G and B, defects were closed by Glubran2 and Bioglue. All animals were euthanized at 28 days postoperative. Stereologic analyses were performed. New bone area and connective tissue volumes were measured. Mean new bone volumes were 0.97 ± 0.28, 0.59 ± 0.2, and 0.8 ± 0.32 mm3 in groups M, G, and B, respectively. The differences between groups were not statistically significant (P > 0.05). In group M, mean connective tissue volumes were 4.25 ± 0.7 mm3, in groups G and B, 2.9 ± 1.82 and 4.54 ± 0.64 mm3. Connective tissue volume differences were not statistically significant between groups. Glubran2 and Bioglue may play a role as a barrier for guided bone regeneration in treatment of critical size defects.
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

We present a de novo assembly of a eukaryote transcriptome using 454 pyrosequencing data. The Glanville fritillary butterfly (Melitaea cinxia; Lepidoptera: Nymphalidae) is a prominent species in population biology but had no previous genomic data. Sequencing runs using two normalized complementary DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608 053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48 354 contigs (sets of overlapping DNA segments) and 59 943 singletons. blast comparisons confirmed the accuracy of the sequencing and assembly, and indicated the presence of c. 9000 unique genes, along with > 6000 additional microarray‐confirmed unannotated contigs. Average depth of coverage was 6.5‐fold for the longest 4800 contigs (348–2849 bp in length), sufficient for detecting large numbers of single nucleotide polymorphisms. Oligonucleotide microarray probes designed from the assembled sequences showed highly repeatable hybridization intensity and revealed biological differences among individuals. We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost‐effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.
Effect of health education on patients' beliefs about glaucoma and compliance.

A pretest-posttest control group experimental design (n = 100) was used to determine the effectiveness of an interactive patient education program compared with a didactic approach for persons with primary open angle glaucoma at a major specialist eye hospital in England. This study used a questionnaire with a knowledge test to explore patients' glaucoma knowledge, a series of vignettes to explore understanding of compliance and health motivation, and health locus of control scales to assess the effect of these variables. The improved posttest results (P = .000) suggest that patients benefit from education programs and that the ophthalmic nurse is an effective patient teacher. The interactive program has no statistically significant difference from the didactic presentation. Other types of interactive programs may prove to be more beneficial.
Joint Carrier Frequency Offset, Sampling Time Offset and Channel Estimation for OFDM-OQAM Systems

Among the alternative multicarrier modulation techniques to orthogonal frequency division multiplexing (OFDM), a derivative of OFDM based on offset quadrature amplitude modulation (OFDM-OQAM) has been one of the most prominent to alleviate the sensitivity problem of the former to timing and frequency mismatch. In this paper, we propose an improved joint estimation method for carrier frequency offset (CFO), sampling time offset (STO) and channel impulse response (CIR) in OFDM-OQAM systems. The proposed method instruments a data-aided maximum-likelihood (ML) joint estimation of the unknown parameters, as derived under an assumption of Gaussian noise and independent input symbols by splitting the interference into pilot, non-pilot and noise terms. Performance evaluation is carried out through simulations by comparing the proposed method with a highly-cited previous work which considers all the three types of parameters in one development. The improvements in the results indicate the superiority of the proposed joint ML-based estimator.
On the well-posedness of LTI networks

We consider networks of linear, time-invariant systems defined over matrices of rational functions in a complex variable where each element of the matrix represents a link in the network. When these rational functions are proper, but not necessarily strictly proper, we demonstrate the necessary and sufficient conditions under which such a network configuration is well-posed. We include multiple examples of network configurations and their respective well-posedness conditions, including cases where two or more ill-posed network configurations can be interconnected to form a well-posed network.