Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal and circadian variation in salivary testosterone in rural Bolivian men

Testosterone (T) plays a key role in the increase and maintenance of muscle mass and bone density in adult men. Life history theory predicts that environmental stress may prompt a reallocation of such investments to those functions critical to survival. We tested this hypothesis in two studies of rural Bolivian adult men by comparing free T levels and circadian rhythms during late winter, which is especially severe, to those in less arduous seasons. For each pair of salivary TAM/TPM samples (collected in a ∼ 12‐h period), circadian rhythm was considered classic (CCLASSIC) if TAM > 110%TPM, reverse (CREVERSE) if TPM > 110%TAM, and flat (CFLAT) otherwise. We tested the hypotheses that mean TAM > mean TPM and that mean TLW < mean TOTHER (LW = late winter, OTHER = other seasons). In Study A, of 115 TPM–TAM pairs, 51% = CCLASSIC, 39% = CREVERSE, 10% = CFLAT; in Study B, of 184 TAM–TPM pairs, 55% = CCLASSIC, 33% = CREVERSE, 12% = CFLAT. Based on fitting linear mixed models, in both studies TOTHER‐AM > TOTHER‐PM (A: P = 0.035, B: P = 0.0005) and TOTHER‐AM > TLW‐AM (A: P = 0.054, B: P = 0.007); TPM did not vary seasonally, and T diurnality was not significant during late winter. T diurnality varied substantially between days within an individual, between individuals and between seasons, but neither T levels nor diurnality varied with age. These patterns may reflect the seasonally varying but unscheduled, life‐long, strenuous physical labor that typifies many non‐industrialized economies. These results also suggest that single morning samples may substantially underestimate peak circulating T for an individual and, most importantly, that exogenous signals may moderate diurnality and the trajectory of age‐related change in the male gonadal axis. Am. J. Hum. Biol., 2009. © 2009 Wiley‐Liss, Inc.
The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the “Functional Genomics in Embryonic Stem Cells” consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in “Expression Waves” and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.
TWORAM: Round-Optimal Oblivious RAM with Applications to Searchable Encryption

We present TWORAM, the first efficient round-optimal oblivious RAM (ORAM) scheme. TWORAM provides oblivious access of a memory index y in exactly two rounds: The client prepares an encrypted query encapsulating y and sends it to the server. The server accesses memory obliviously and returns encrypted information containing the desired value M[y]. The cost of TWORAM is only a multiplicative factor of security parameter higher than the tree-based ORAM schemes such as the path ORAM of Stefanov et al. (CCS, 2013). TWORAM gives rise to interesting applications, and in particular to the first fully-secure searchable symmetric encryption scheme where search is sublinear and search pattern is not leaked—access pattern can also be concealed if we assume the documents are stored in the obliviously accessed memory M.
The Involvement of Calcium and MAP Kinase Signaling Pathways in the Production of Radiation-Induced Bystander Effects

Abstract Lyng, F. M. , Maguire, P., McClean, B. , Seymour, C. and Mothersill, C. The Involvement of Calcium and MAP Kinase Signaling Pathways in the Production of Radiation-Induced Bystander Effects. Radiat. Res. 165, 400–409 (2006). Much evidence now exists regarding radiation-induced bystander effects, but the mechanisms involved in the transduction of the signal are still unclear. The mitogen-activated protein kinase (MAPK) pathways have been linked to growth factor-mediated regulation of cellular events such as proliferation, senescence, differentiation and apoptosis. Activation of multiple MAPK pathways such as the ERK, JNK and p38 pathways have been shown to occur after exposure of cells to radiation and a variety of other toxic stresses. Previous studies have shown oxidative stress and calcium signaling to be important in radiation-induced bystander effects. The aim of the present study was to investigate MAPK signaling pathways in bystander cells exposed to irradiated cell conditioned medium (ICCM) and the role of oxidative metabolism and calcium signaling in the induction of bystander responses. Human keratinocytes (HPV-G cell line) were irradiated (0.005–5 Gy) using a cobalt-60 teletherapy unit. The medium was harvested 1 h postirradiation and transferred to recipient HPV-G cells. Phosphorylated forms of p38, JNK and ERK were studied by immunofluorescence 30 min–24 h after exposure to ICCM. Inhibitors of the ERK pathway (PD98059 and U0126), the JNK pathway (SP600125), and the p38 pathway (SB203580) were used to investigate whether bystander-induced cell death could be blocked. Cells were also incubated with ICCM in the presence of superoxide dismutase, catalase, EGTA, verapamil, nifedipine and thapsigargin to investigate whether bystander effects could be inhibited because of the known effects on calcium homeostasis. Activated forms of JNK and ERK proteins were observed after exposure to ICCM. Inhibition of the ERK pathway appeared to increase bystander-induced apoptosis, while inhibition of the JNK pathway appeared to decrease apoptosis. In addition, reactive oxygen species, such as superoxide and hydrogen peroxide, and calcium signaling were found to be important modulators of bystander responses. Further investigations of these signaling pathways may aid in the identification of novel therapeutic targets.
On the notion of variability in software product lines

The authors discuss the notion of variability. We have experienced that this concept has so far been underdefined, although we have observed that variability techniques become increasingly important. A clear indication of this trend is the recent emergence of software product lines. Software product lines are large, industrial software systems intended to specialize into specific software products. The authors provide a framework of terminology and concepts regarding variability. In addition, they present three recurring patterns of variability. Finally, they suggest a method for managing variability in software product lines.
Chronic obstructive pulmonary disease phenotypes: the future of COPD.

Significant heterogeneity of clinical presentation and disease progression exists within chronic obstructive pulmonary disease (COPD). Although FEV(1) inadequately describes this heterogeneity, a clear alternative has not emerged. The goal of phenotyping is to identify patient groups with unique prognostic or therapeutic characteristics, but significant variation and confusion surrounds use of the term "phenotype" in COPD. Phenotype classically refers to any observable characteristic of an organism, and up until now, multiple disease characteristics have been termed COPD phenotypes. We, however, propose the following variation on this definition: "a single or combination of disease attributes that describe differences between individuals with COPD as they relate to clinically meaningful outcomes (symptoms, exacerbations, response to therapy, rate of disease progression, or death). " This more focused definition allows for classification of patients into distinct prognostic and therapeutic subgroups for both clinical and research purposes. Ideally, individuals sharing a unique phenotype would also ultimately be determined to have a similar underlying biologic or physiologic mechanism(s) to guide the development of therapy where possible. It follows that any proposed phenotype, whether defined by symptoms, radiography, physiology, or cellular or molecular fingerprint will require an iterative validation process in which "candidate" phenotypes are identified before their relevance to clinical outcome is determined. Although this schema represents an ideal construct, we acknowledge any phenotype may be etiologically heterogeneous and that any one individual may manifest multiple phenotypes. We have much yet to learn, but establishing a common language for future research will facilitate our understanding and management of the complexity implicit to this disease.
Genetic variation in a Pacific Island land snail: population history versus current drift and selection

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that there can be striking differences in shell shape, colour and banding pattern between nearby populations, even in the absence of any obvious geographical barriers to the movement of snails, or environmental gradients. Elsewhere, there may be relative uniformity over large distances. Analysis of a mitochondrial gene from Partula taeniata (Mörch) shows a similar pattern. The relative frequencies of two mitochondrial haplotypes change abruptly over small distances, seemingly independent of the environment. Although the transition roughly coincides with clines in the frequencies of some morphological characteristics, it appears to be unrelated to others. It is likely that many of the differences accumulated while populations were isolated from one another, through the effects of random genetic drift and selection. Isolation of populations may have occurred as a result of demographic changes, or during the process of colonization if occasional long-distance migrants establish populations ahead of the main invading front. Current genetic drift, even without restrictions to gene flow, may contribute to genetic patchiness on a small scale, although it is likely that conspicuous characteristics such as shell colours and banding patterns are also influenced by selection.
MHC Adaptive Divergence between Closely Related and Sympatric African Cichlids

Background The haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa. Methodology/Principal Findings Divergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS) amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites. Conclusions/Significance We propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.
Vaccinia Virus 15-Kilodalton (A14L) Protein Is Essential for Assembly and Attachment of Viral Crescents to Virosomes

ABSTRACT Early stages in vaccinia virus (VV) assembly involve the recruitment of cellular membranes from the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) to virus factories (or virosomes). The key viral factors involved in this process are not yet known. We have previously identified and characterized two viral proteins, of 21 kDa (A17L gene) and 15 kDa (A14L gene), that associate with tubulovesicular elements related to the ERGIC and are localized in viral membranes at all stages of virion assembly. We showed that the 21-kDa protein is not responsible for the recruitment of membranes from the ERGIC to viral factories. However, it appears to be essential for the organization of viral membranes. In this investigation we have generated a VV recombinant, VVindA14L, in which the expression of the A14L gene is inducibly regulated by the Escherichia coli lacIoperator-repressor system. Repression of 15-kDa protein synthesis has a dramatic effect on virus yields and severely impairs plaque formation. Compared to wild-type VV, reduced amounts of 15-kDa protein are produced in VVindA14L-infected cells in the presence of IPTG (isopropyl-β-d-thiogalactoside), and this correlates with a small-plaque phenotype and reduced VVindA14L yields under these conditions. In the absence of the 15-kDa protein, early and late viral protein syntheses proceed normally; however, proteolytic cleavage of the major core precursors is inhibited. Electron microscopic examination of cells infected with VVindA14L under nonpermissive conditions reveals the presence of numerous membranous elements that look like unfinished or disassembled crescents interespersed between electron-dense masses. These abnormal membrane elements are usually well separated from the surfaces of the dense structures. These findings show that the 15-kDa protein is essential for VV morphogenesis and indicate that this polypeptide is necessary both for the correct assembly of viral crescents and for their stable attachment to the surfaces of viral factories.
Investigating of high and low impact faults in object-oriented projects

For optimum utilization of resources and reducing the cost of software, the fault detection and elimination process must be properly planned and for this type of planning prediction of fault-prone module is gaining importance among researchers. It would be valuable to know how object-oriented design metrics and class fault-proneness are related when fault impact is taken into account. In this paper, we use the logistic regression method to empirically investigate the usefulness of object-oriented design metrics in predicting fault-proneness when taking fault impact into account. Our results, based on a public domain NASA Promise data set, indicate that most of these design metrics are statistically related to fault-proneness of classes across fault impact, and the prediction capabilities of the investigated metrics greatly depend on the impact of faults. More specifically, these design metrics are able to predict high/low impact faults in fault-prone classes.
Relaxed Failure Recovery Process for Reliable Quality-of-Service using Unreserved Backup Paths

Guaranteed, high-quality service in the computer network often requires a single reserved path. However, a single path can easily suffer from single point failures. This paper provides a solution to handle flows when their reserved primary paths fail. The solution pairs a reserved primary path with an unreserved backup path. When a failure occurs and a primary path fails, the initial service guarantee is relaxed slightly, and the flow with the failed primary path is re-routed on the least congested alternate path. This approach allows all flows to continue despite a failure in the network. In addition, even though the service quality is relaxed to accommodate flows with failed primary paths, by carefully planning the least congested alternate paths as backups, very high levels of service quality can still be retained after failure.
On Quality Ratings for Spoken Dialogue Systems – Experts vs. Users

In the field of Intelligent User Interfaces, Spoken Dialogue Systems (SDSs) play a key role as speech represents a true intuitive means of human communication. Deriving information about its quality can help rendering SDSs more user-adaptive. Work on automatic estimation of subjective quality usually relies on statistical models. To create those, manual data annotation is required, which may be performed by actual users or by experts. Here, both variants have their advantages and drawbacks. In this paper, we analyze the relationship between user and expert ratings by investigating models which combine the advantages of both types of ratings. We explore two novel approaches using statistical classification methods and evaluate those with a preexisting corpus providing user and expert ratings. After analyzing the results, we eventually recommend to use expert ratings instead of user ratings in general.
[Placental leptin correlates with intrauterine fetal growth and development].

OBJECTIVE To study the role of placental leptin in intrauterine cord leptin production and its relationship with neonatal anthropometry. METHODS Forty women and their babies were enrolled and approved by Xinhua Hospital (Shanghai, China) and Jiangbei Hospital (Nanjing, China) in this study. Placental tissue was assayed for leptin mRNA by reverse transcription/polymerase chain reaction (RT/PCR), and assayed for ob gene protein, leptin, by Western-Blot and immunohistochemistry. Blood was taken from the umbilical cord of the babies at delivery. Serum leptin was measured by radio-immunoassay. Neonatal anthropometric measurements were recorded within 48 hours after delivery. Linear regression analysis was used to explore the relationship between placental leptin, cord leptin and neonatal anthropometric measures. RESULTS Ob gene was expressed in placental tissue at comparable or greater levels than that in adipose tissue. Comparison of the relative levels of leptin to beta-actin mRNA by multiplex RT/PCR revealed that the placenta of the small for gestational age (SGA) neonates expressed leptin mRNA at significantly lower levels 0.61 +/- 0.15 than that of the appropriate for gestational age (AGA) neonates 0.83 +/- 0.20 (P = 0.0034), while the placenta of the large for gestational age (LGA) neonates expressed leptin mRNA at significantly higher levels 1.00 +/- 0.23 than that of the AGA neonates (P = 0.043). Immunohistochemical techniques showed the immunostaining pattern in the cytoplasm of trophoblastic cells. Western-blot showed that the placenta of the SGA neonates expressed leptin at significantly lower levels 0.26 +/- 0.05 ng/mg than that of the AGA neonates 0.34 +/- 0.09 ng/mg (P = 0.007 6), while the placenta of the LGA neonates expressed leptin at significantly higher levels 0.43 +/- 0.10 ng/mg than that of the AGA neonates (P = 0.021). Linear regression analysis showed placental ob gene transcription and leptin translation correlated significantly with cord leptin (r = 0.39 and 0.43), and neonatal Ponderal Index (r = 0.66 and 0.69). CONCLUSIONS Placenta provides a source of leptin for the growing fetus, and this placental leptin might be a growth factor in intrauterine fetal development.
Preanalytical and Postanalytical Variables: The Leading Causes of Diagnostic Error in Hemostasis?

The advent of modern instrumentation, with associated improvements in test reliability, together with appropriate internal quality control and external quality assurance measures, has led to substantial reduction in analytical errors within hemostasis laboratories. Unfortunately, the reporting of incorrect or inappropriate test results still occurs, perhaps even as frequently as in the past. Many of these cases will arise due to a variety of events largely outside the control of the laboratories performing the laboratory tests and primarily comprise preanalytical events related to patient collection and sample processing and postanalytical events related to the reporting and interpretation of test results. The current article provides an overview of these events and provides some suggestions on how they can be minimized or prevented to ensure that the test results the clinician receives actually represent the true clinical status of the patient under investigation rather than just reflecting the status of an (inappropriate) clinical sample received and tested. This article should be of interest to both laboratory scientists working in hemostasis and the clinicians that request such tests. The former, because these are ultimately responsible for the test results they provide to clinicians, and there is a duty of care to provide both accurate and precise results to enable clinicians to manage patients appropriately and to avoid the need to recollect and retest. The latter because unless clinicians gain an appreciation of these issues, they will not be in a position to best manage their patients.
Economic Impact of Dengue Illness in the Americas

The growing burden of dengue in endemic countries and outbreaks in previously unaffected countries stress the need to assess the economic impact of this disease. This paper synthesizes existing studies to calculate the economic burden of dengue illness in the Americas from a societal perspective. Major data sources include national case reporting data from 2000 to 2007, prospective cost of illness studies, and analyses quantifying underreporting in national routine surveillance systems. Dengue illness in the Americas was estimated to cost $2.1 billion per year on average (in 2010 US dollars), with a range of $1–4 billion in sensitivity analyses and substantial year to year variation. The results highlight the substantial economic burden from dengue in the Americas. The burden for dengue exceeds that from other viral illnesses, such as human papillomavirus (HPV) or rotavirus. Because this study does not include some components (e.g., vector control), it may still underestimate total economic consequences of dengue.
OSSS+R: Modelling and Simulating Self-Reconfigurable Systems

High level description languages and tools lack appropriate support to specify reconfigurable systems. We propose a methodology for partially self-reconfigurable systems, which consists of a SystemC based language, simulation abilities and the perspective of automated synthesis. We introduce a configuration management infrastructure, which frees designers of error-prone and time consuming tasks
Low-Power, Secure Routing for MICA2 Mote

Current distributed sensor network platforms lack comprehensive lowpower routing techniques and efficient public key cryptography mechanisms. Reducing power for individual radio transmissions has not been explored sufficiently. Popular sensor node platforms do not include a mechanism for distributing and redistributing shared cryptographic keys among nodes. This paper discusses a technique to tailor node transmit power to the lowest practical level while maintaining reliable network links and presents the first known implementation of elliptic curve cryptography for sensor networks. Results demonstrate that dynamic radio output power scaling is effective in reducing node power consumption by orders of magnitude in certain scenarios. Analysis suggests that secret-key cryptography is already viable on the UC Berkeley MICA2 mote and public-key infrastructure may also be tractable despite the device’s limited memory.