Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular Proton Regulation of ClC-0

Some CLC proteins function as passive Cl− ion channels whereas others are secondary active chloride/proton antiporters. Voltage-dependent gating of the model Torpedo channel ClC-0 is modulated by intracellular and extracellular pH, possibly reflecting a mechanistic relationship with the chloride/proton coupling of CLC antiporters. We used inside-out patch clamp measurements and mutagenesis to explore the dependence of the fast gating mechanism of ClC-0 on intracellular pH and to identify the putative intracellular proton acceptor(s). Among the tested residues (S123, K129, R133, K149, E166, F214L, S224, E226, V227, C229, R305, R312, C415, H472, F418, V419, P420, and Y512) only mutants of E166, F214, and F418 qualitatively changed the pHint dependence. No tested amino acid emerged as a valid candidate for being a pH sensor. A detailed kinetic analysis of the dependence of fast gate relaxations on pHint and [Cl−]int provided quantitative constraints on possible mechanistic models of gating. In one particular model, a proton is generated by the dissociation of a water molecule in an intrapore chloride ion binding site. The proton is delivered to the side chain of E166 leading to the opening of the channel, while the hydroxyl ion is stabilized in the internal/central anion binding site. Deuterium isotope effects confirm that proton transfer is rate limiting for fast gate opening and that channel closure depends mostly on the concentration of OH− ions. The gating model is in natural agreement with the finding that only the closing rate constant, but not the opening rate constant, depends on pHint and [Cl−]int.
Creak: Color-based retina keypoint descriptor

Effectively feature matching between images is key to many computer vision applications. Recently, binary descriptors are attracting increasing attention for their low computational complexity and small memory requirement. However, most binary descriptors are based on intensity comparisons of grayscale images and did not consider color information. In this paper, a novel binary descriptor inspired by human retina is proposed, which considers not only gray values of pixels but also color information. Experimental results show that the proposed feature descriptor spends fewer storage spaces while having better precision level than other popular binary descriptors. Besides, the proposed feature descriptor has the fastest matching speed among all the descriptors under comparison, which makes it suitable for realtime applications.
Management of narcolepsy

Background: Narcolepsy is a rare chronic sleep disorder classically characterized by excessive daytime sleepiness. Other symptoms of the disease, including cataplexy, sleep paralysis, hypnagogic hallucinations and disturbed nocturnal sleep, may follow later. The disease can be incapacitating and frequently results in impaired psychosocial interaction. In the absence of a cure for narcolepsy, medical therapy is directed at symptom control. Objectives: The aim of this study was to review the current approach to the treatment of narcolepsy. Methods: A search of three bibliographic databases (MEDLINE/PubMed, EMBASE and the Cochrane Library Database) was conducted from 1966 to January 2008 using the National Library of Medicine MeSH search terms narcolepsy and cataplexy. Relevant studies, case reports, review articles, editorials, short communications and chapters from selected textbooks were then extracted and manually cross-referenced. Results/conclusions: Traditionally, stimulants have been used to improve the symptoms of excessive daytime sleepiness. However, the treatment of narcolepsy has evolved recently with the widespread use of newer drugs, including modafinil for daytime sleepiness, newer antidepressants for cataplexy and γ-hydroxybutyrate (sodium oxybate) for both excessive daytime sleepiness and cataplexy.
DNA methylation and demethylation events during meiotic prophase in the mouse testis

The genes encoding three different mammalian testis-specific nuclear chromatin proteins, mouse transition protein 1, mouse protamine 1, and mouse protamine 2, all of which are expressed postmeiotically, are marked by methylation early during spermatogenesis in the mouse. Analysis of DNA from the testes of prepubertal mice and isolated testicular cells revealed that transition protein 1 became progressively less methylated during spermatogenesis, while the two protamines became progressively more methylated; in contrast, the methylation of beta-actin, a gene expressed throughout spermatogenesis, did not change. These findings provide evidence that both de novo methylation and demethylation events are occurring after the completion of DNA replication, during meiotic prophase in the mouse testis.
Assessing the risk of breast cancer.

Each year in the United States, breast cancer is diagnosed in more than 170,000 women.1 Despite this substantial burden of disease, however, assessment of breast-cancer risk has received very little attention outside the oncology clinic.2,3 In primary care, the main result of the recognition of individual variation in breast-cancer risk is the use of age to determine recommendations regarding mammography (older age is a strong risk factor for breast cancer). 4 Recent developments in the ability to predict and alter breast-cancer risk warrant a new look at the role of assessment of this risk in primary care. Physicians must become .
Fusion of face and speech data for person identity verification

Biometric person identity authentication is gaining more and more attention. The authentication task performed by an expert is a binary classification problem: reject or accept identity claim. Combining experts, each based on a different modality (speech, face, fingerprint, etc.), increases the performance and robustness of identity authentication systems. In this context, a key issue is the fusion of the different experts for taking a final decision (i.e., accept or reject identity claim). We propose to evaluate different binary classification schemes (support vector machine, multilayer perceptron, C4.5 decision tree, Fisher's linear discriminant, Bayesian classifier) to carry on the fusion. The experimental results show that support vector machines and Bayesian classifier achieve almost the same performances, and both outperform the other evaluated classifiers.
Weisfeiler-Lehman Graph Kernels

In this article, we propose a family of efficient kernels for large graphs with discrete node labels. Key to our method is a rapid feature extraction scheme based on the Weisfeiler-Lehman test of isomorphism on graphs. It maps the original graph to a sequence of graphs, whose node attributes capture topological and label information. A family of kernels can be defined based on this Weisfeiler-Lehman sequence of graphs, including a highly efficient kernel comparing subtree-like patterns. Its runtime scales only linearly in the number of edges of the graphs and the length of the Weisfeiler-Lehman graph sequence. In our experimental evaluation, our kernels outperform state-of-the-art graph kernels on several graph classification benchmark data sets in terms of accuracy and runtime. Our kernels open the door to large-scale applications of graph kernels in various disciplines such as computational biology and social network analysis.
Use of cell-site diversity in millimeter-wave fixed cellular systems to combat the effects of rain attenuation

An examination of potential advantages of cell-site diversity with selection combining in the context of MM-wave fixed cellular systems is reported. The study involves simulation of converging radio links over weather radar images of the radar reflectivity factor, from which the specific attenuation of rain at 30 GHz is derived. The average correlation of attenuation on two converging links as a function of their angular separation is shown to indicate the potential benefits in the use of cell-site diversity, especially in heavy rain. Results show that diversity gain exhibits a dependence on angular separation /spl theta/ in the general form of sin/sup k/ (/spl theta//2). For links of identical lengths the model reduces to a root-sinusoidal shape (k=0.5), whereas links of unequal lengths lead to the ITU-R recommended model (k=1). Based on the sin/sup k/ (/spl theta//2) model and observation of the length ratio of the links, a set of criteria for determining the benefit of cell-site diversity for a given subscriber location is proposed.
Psychosocial factors associated with the effects of physiotherapy in the acute hospital

Purpose. To examine the associations between psychosocial factors and physical functioning at admission, and functional recovery during an acute hospital admission. Method. Included into this multi-centre cohort study were 642 patients with cardiopulmonary, musculoskeletal and neurological conditions recruited from 32 Swiss hospitals. Functional status was measured at admission and discharge using the Barthel Index (BI); BI change was used as an indicator for functional recovery. Sense of coherence (SOC) and depression were assessed at admission using the SOC questionnaire and the Hospital Anxiety and Depression Scale (HADS); patient motivation was judged at discharge by physiotherapists on a Visual Analogue Scale. Mixed effect regression was used to assess associations of SOC, depression and motivation with functional status at admission and functional recovery. Distinct models were built to control for sets of behavioural, socio-economic and disease-related variables. Results. Functional status at admission was significantly associated with SOC, depression and motivation. Functional recovery was significantly associated with motivation, but not with SOC. Significant associations between functional recovery and depression were found in some of the models. Conclusions. As motivation showed strong associations with functional recovery, future studies should examine how functional recovery is influenced by motivation and how motivation can be improved.
Knee alignment differences between Chinese and Caucasian subjects without osteoarthritis

Objective: Despite the lower prevalence of obesity (a known risk factor for osteoarthritis (OA)), the prevalence of lateral tibiofemoral OA is higher in Chinese communities compared with Caucasian communities. One potential explanation is the difference in knee alignment between the two populations. We measured various knee alignment indices among Chinese and Caucasians and assessed whether these indices were different between the two racial groups. Methods: We selected participants from the Framingham Osteoarthritis Study (FOA) and the Beijing Osteoarthritis Study (BOA), all without knee OA (Kellgren & Lawrence grade <2). Bilateral, fully extended anteroposterior knee radiographs were measured for the following angles in both knees: the anatomic axis (AA), the condylar angle (CA), the tibial plateau angle and the condylar–plateau angle (CP). We compared the mean of each measurement between the two racial groups adjusting for age and body mass index using linear regression and stratified by sex. Results: The mean AA, CA and CP were significantly different in the BOA compared with the FOA. For women, the mean AA and CA were significantly more valgus in BOA subjects, while in men, the mean AA and CP were more valgus in BOA subjects. Conclusions: There are significant differences in knee morphology between Chinese and Caucasian cohorts, which result in a more valgus alignment of the distal femur in Chinese. This would serve to shift the mechanical loading towards the lateral compartment, and provide a possible explanation why Chinese have a higher prevalence of lateral tibiofemoral OA.
Estimation of $n$ Frequencies Using Adaptive Notch Filter

This paper introduces an adaptive structure composed of n coupled paralleled subfilters that directly estimates frequencies of multiple sinusoids. The order of differential equations governing this algorithm is 3n, where n is the number of sinusoids. Stability analysis of this algorithm is carried out based on the application of the averaging theory under the assumption of the slow adaptation. Simulation results verify the validity of the analytical issues
Countering Wrapping Attack on XML Signature in SOAP Message for Cloud Computing

It is known that the exchange of information between web applications is done by means of the SOAP protocol. Securing this protocol is obviously a vital issue for any computer network. However, when it comes to cloud computing systems, the sensitivity of this issue rises, as the clients of system, release their data to the cloud. XML signature is employed to secure SOAP messages. However, there are also some weak points that have been identified, named as XML signature wrapping attacks, which have been categorized into four major groups; Simple Ancestry Context Attack, Optional element context attacks, Sibling Value Context Attack, Sibling Order Context. In this paper, two existing methods, for referencing the signed part of SOAP Message, named as ID referencing and XPath method, are analyzed and examined. In addition, a new method is proposed and tested, to secure the SOAP message. In the new method, the XML any signature wrapping attack is prevented by employing the concept of XML digital signature on the SOAP message. The results of conducted experiments show that the proposed method is approximately three times faster than the XPath method and even a little faster than ID.
The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain

SUMMARY In honey bees, vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. MicroRNAs, which play important roles in post-transcriptional gene regulation, likewise affect many biological processes. The actions of microRNAs and Vg are known to intersect in the context of reproduction; however, the role of these associations on social behavior is unknown. The phenotypic effects of Vg knockdown are best established and studied in the forager stage of workers. Thus, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its downstream effects on microRNA population in honey bee foragers' brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used μParaflo microfluidic oligonucleotide microRNA microarrays. Our results showed that 76 and 74 microRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 microRNAs were expressed in the fat body of control and knockdown foragers, respectively. Target prediction identified potential seed matches for a differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between the Vg knockdown forager phenotype and variation in the abundance of microRNAs in different tissues, with possible consequences for the regulation of foraging behavior.
Central Bank Refinancing, Interbank Markets and the Hypothesis of Liquidity Hoarding: Evidence from a Euro-Area Banking System

This paper tests the hypothesis of liquidity hoarding in the Italian banking system during the 2007-2011 global financial crisis. According to this hypothesis, in periods of crisis, interbank markets stop working and central banksi? ½ interventions are ineffective because banks hoard the liquidity injected rather than channelling it on to other banks and the real economy. The test uses monthly data at banking-group level for all intermediaries operating in Italy between January 1999 and August 2011. This is the first paper to use micro data to analyse the relationship between single banksi? ½ positions vis-i? ½-vis the central bank and the interbank market. The results show that the Italian interbank market functioned well even during the crisis, and, contrary to widespread conjecture, the liquidity injected by the Eurosystem was intermediated among banks and towards the real economy. This finding is robust to the use of several estimation methods and data on the different segments of the money market.
Probing the Run-On Oligomer of Activated SgrAI Bound to DNA

SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved), and also binds (and thereby activates for DNA cleavage) complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3’-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.
Inactivating UBE2M Impacts the DNA Damage Response and Genome Integrity Involving Multiple Cullin Ligases

Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.
Contacts and edge-state equilibration in the fractional quantum Hall effect.

We develop a simple kinetic equation description of edge state dynamics in the fractional quantum Hall effect (FQHE), which allows us to examine in detail equilibration processes between multiple edge modes. As in the integer quantum Hall effect (IQHE), inter-mode equilibration is a prerequisite for quantization of the Hall conductance. Two sources for such equilibration are considered: Edge impurity scattering and equilibration by the electrical contacts. Several specific models for electrical contacts are introduced and analyzed. For FQHE states in which edge channels move in both directions, such as $\nu=2/3$, these models for the electrical contacts {\it do not} equilibrate the edge modes, resulting in a non-quantized Hall conductance, even in a four-terminal measurement. Inclusion of edge-impurity scattering, which {\it directly} transfers charge between channels, is shown to restore the four-terminal quantized conductance. For specific filling factors, notably $\nu =4/5$ and $\nu=4/3$, the equilibration length due to impurity scattering diverges in the zero temperature limit, which should lead to a breakdown of quantization for small samples at low temperatures. Experimental implications are discussed.
Infant Body Composition and Adipokine Concentrations in Relation to Maternal Gestational Weight Gain

OBJECTIVE To investigate associations of maternal gestational weight gain and body composition and their impact on offspring body composition and adipocytokine, glucose, and insulin concentrations at age 4 months. RESEARCH DESIGN AND METHODS This was a prospective study including 31 mother-infant pairs (N = 62). Maternal body composition was assessed using doubly labeled water. Infant body composition was assessed at 4 months using air displacement plethysmography, and venous blood was assayed for glucose, insulin, adiponectin, interleukin-6 (IL-6), and leptin concentrations. RESULTS Rate of gestational weight gain in midpregnancy was significantly associated with infant fat mass (r = 0.41, P = 0.03); rate of gestational weight in late pregnancy was significantly associated with infant fat-free mass (r = 0.37, P = 0.04). Infant birth weight was also strongly correlated with infant fat-free mass at 4 months (r = 0.63, P = 0.0002). Maternal BMI and maternal fat mass were strongly inversely associated with infant IL-6 concentrations (r = −0.60, P = 0.002 and r = −0.52, P = 0.01, respectively). Infant fat-free mass was inversely related to infant adiponectin concentrations (r = −0.48, P = 0.008) and positively correlated with infant blood glucose adjusted for insulin concentrations (r = 0.42, P = 0.04). No significant associations for leptin were observed. CONCLUSIONS Timing of maternal weight gain differentially impacts body composition of the 4-month-old infant, which in turn appears to affect the infant’s glucose and adipokine concentrations.
IntegraL: An Effective Link-based Federated Search Infrastructure

This research provides a new means for making digital library services interoperable. IntegraL facilitates a virtual restructuring of public web spaces and services, bringing authenticated digital libraries into broad “federated” digital library spaces constructed from numerous interrelationships. Elements of users’ search interests reside within a rich context of meta-information that helps users understand and work with them. This provides a ripe environment for organizations and individual people to develop small, specialized collections and services, which automatically become part of the federated space and accessible to those they can benefit. IntegraL extends the boundaries of how we think about and interact with digital libraries.
The most probable database problem

This paper proposes a novel inference task for probabilistic databases: the most probable database (MPD) problem. The MPD is the most probable deterministic database where a given query or constraint is true. We highlight two distinctive applications, in database repair of key and dependency constraints, and in finding most probable explanations in statistical relational learning. The MPD problem raises new theoretical questions, such as the possibility of a dichotomy theorem for MPD, classifying queries as being either PTIME or NP-hard. We show that such a dichotomy would diverge from dichotomies for other inference tasks. We then prove a dichotomy for queries that represent unary functional dependency constraints. Finally, we discuss symmetric probabilities and the opportunities for lifted inference.