Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Immobilization in Alginate on the Stability of Freeze-Dried Bifidobacterium longum

Bifidobacterium longum RO23 was immobilized in calcium alginate gels and freeze-dried. The effects of immobilization, storage temperature and composition of the protective solution were studied. High mortality (two log reduction in viable count) was observed when a concentrated culture was immobilized and immediately freeze-dried. Such and immobilization procedure also reduced stability during storage at 20°C. This feature was strain/species related, as immobilization in alginate beads was not detrimental to the survival of Lactococcus lactis RO58 and Lactobacillus rhamnosus RO11 to freeze-drying, but influenced negatively Streptococcus thermophilus RO57. Alginate and calcium chloride, used in the immobilization process, were not responsible for the high mortality of immobilized B. longum RO23. Bifidobacteria grown in the alginate beads did not produce high post-lyophilization mortality, suggesting that freeze-drying the culture immediately following immobilization was the cause of the high mortality, and exposing the cells to a growth medium between immobilization and freeze-drying may allow recovery. Whey-based protective solutions that are mixed to the alginate beads were more effective than milk-based solutions in protecting the immobilized cells against mortality during freeze-drying.
Investigation of window size in classification of EEG-emotion signal with wavelet entropy and support vector machine

When dealing with patients with psychological or emotional symptoms, medical practitioners are often faced with the problem of objectively recognizing their patients' emotional state. In this paper, we approach this problem using a computer program that automatically extracts emotions from EEG signals. We extend the finding of Koelstra et. al [IEEE trans. affective comput. , vol. 3, no. 1, pp. 18-31, 2012] using the same dataset (i.e. the DEAP: dataset for emotion analysis using electroencephalogram, physiological and video signals), where we observed that the accuracy can be further improved using wavelet features extracted from shorter time segments. More precisely, we achieved accuracy of 65% for both valence and arousal using the wavelet entropy of 3 to 12 seconds signal segments. This improvement in accuracy entails an important discovery that information on emotions contained in the EEG signal may be better described in term of wavelets and in shorter time segments.
Oral Anticoagulants

HISTORY OF ORAL ANTICOAGULATION The discovery of oral medications to control thrombotic disorders in humans probably started with a report in 1922 by U.S. veterinarian Frank W Schofield. Dr Schofield reported a bleeding diathesis in cattle that simulated hemorrhagic septicemia and “black leg syndrome”. He hypothesized that this disorder was due to feeding spoiled sweet clover to the cattle.1 In 1935, while studying the sterol metabolism of chicks in Copenhagen, 1943 Nobel Prize winner Henrik Dam discovered a bleeding tendency in the chicks fed a diet deficient in lipids. These results suggested the chicks lacked a substance necessary for normal coagulation; “Koagulations-Vitamin” or vitamin K. He studied this vitamin further with respect to its occurrence and biological function in animals and plants as well as its application in human medicine.2 In 1933 a Wisconsin farmer arrived at Karl Paul Link's laboratory at the University of Wisconsin-Madison with a pail of blood that would not coagulate. He also brought a small heap of spoiled sweet clover and a dead heifer in the back of his truck. Isolation and purification of the hemorrhagic compound led to the discovery of dicumarol (3,3-methylene-bis- {4-hyroxycoumarin}). 3 Clinical studies were immediately started on this compound, establishing the basis for rodenticides and the first oral anticoagulant. The compound greatly diminished prothrombin activity and delayed the clotting mechanism in blood. The first prophylactic and therapeutic effects and the drug's mechanism in influencing deep vein thrombosis were described in 1942.4-6 Link, in 1948, went to the director of the Wisconsin… ABBREVIATIONS: AMS = anticoagulation management service; DVT = deep vein thrombosis; GLA = gamma-carboxyl glutamic acid; GLU = glutamic acid; INR = international normalized ratio; IRP = international reference plasma; ISI = international sensitivity index; OAT = oral anticoagulant therapy; POC = point-of-care device; PT = prothrombin time; VTE = venous thromboembolism; WHO = World Health Organization.
Cellular Localization and Role of Prohormone Convertases in the Processing of Pro-melanin Concentrating Hormone in Mammals*

Melanin concentrating hormone (MCH) and neuropeptide EI (NEI) are two peptides produced from the same precursor in mammals, by cleavage at the Arg145-Arg146 site and the Lys129-Arg130 site, respectively. We performed co-localization studies to reveal simultaneously the expression of MCH mRNA and proconvertases (PCs) such as PC1/3 or PC2. In the rat hypothalamus, PC2 was present in all MCH neurons, and PC1/3 was present in about 15–20% of these cells. PC1/3 or PC2 was not found in MCH-positive cells in the spleen. In GH4C1cells co-infected with vaccinia virus (VV):pro-MCH along with VV:furin, PACE4, PC1/3, PC2, PC5/6A, PC5/6B, or PC7, we observed only efficient cleavage at the Arg145-Arg146 site to generate mature MCH. Co-expression of pro-MCH together with PC2 and 7B2 resulted in very weak processing to NEI. Comparison of pro-MCH processing patterns in PC1/3- or PC2-transfected PC12 cells showed that PC2 but not PC1/3 generated NEI. Finally, we analyzed the pattern of pro-MCH processing in PC2 null mice. In the brain of homozygotic mutants, the production of mature NEI was dramatically reduced. In contrast, MCH content was increased in the hypothalamus of PC2 null mice. In the spleen, a single large MCH-containing peptide was identified in both wild type and PC2 null mice. Together, our data suggest that pro-MCH is processed differently in the brain and in peripheral organs of mammals. PC2 is the key enzyme that produces NEI, whereas several PCs may cleave at the Arg145-Arg146 site to generate MCH in neuronal cell types.
Acute hypoglycemia impairs nonverbal intelligence: importance of avoiding ceiling effects in cognitive function testing.

Acute hypoglycemia causes a progressive, reversible deterioration in cognitive function that becomes detectable at blood glucose concentrations below ∼3.0–3.4 mmol/l (1). In an earlier study in nondiabetic subjects, we reported that several facets of attention deteriorated significantly at an arterialized blood glucose level of 2.6 mmol/l (2). However, performance on Raven’s Progressive Matrices (RPM) was not significantly impaired at either 20 min or completion of the test (with no time limit). This was unexpected, because, previously, various domains of cognitive function had consistently been impaired at this level of hypoglycemia (1). Additionally, the RPM is acknowledged as being among the best indicators of general fluid intelligence (3) and has a substantial correlation with working memory (4), which is exquisitely sensitive to hypoglycemia (5). Hypoglycemia disrupts performance on different cognitive function tests to a variable degree, leading to speculation that different mental functions vary …
Spectral Domain Speech Enhancement Using HMM State-Dependent Super-Gaussian Priors

The derivation of MMSE estimators for the DFT coefficients of speech signals, given an observed noisy signal and super-Gaussian prior distributions, has received a lot of interest recently. In this letter, we look at the distribution of the periodogram coefficients of different phonemes, and show that they have a gamma distribution with shape parameters less than one. This verifies that the DFT coefficients for not only the whole speech signal but also for individual phonemes have super-Gaussian distributions. We develop a spectral domain speech enhancement algorithm, and derive hidden Markov model (HMM) based MMSE estimators for speech periodogram coefficients under this gamma assumption in both a high uniform resolution and a reduced-resolution Mel domain. The simulations show that the performance is improved using a gamma distribution compared to the exponential case. Moreover, we show that, even though beneficial in some aspects, the Mel-domain processing does not lead to better results than the algorithms in the high-resolution domain.
Menstrual Cycle and Competitive Bidding

In an experiment using two-bidder first-price sealed bid auctions with symmetric independent private values, we collected information on the female participants' menstrual cycles. We find that women bid significantly higher than men in their menstrual and premenstrual phase but do not bid significantly different in other phases of the menstrual cycle. We suggest an evolutionary hypothesis according to which women are genetically predisposed by hormones to generally behave more riskily during their fertile phase of their menstrual cycle in order to increase the probability of conception, quality of offspring, and genetic variety. Our finding is in contrast to results by Chen, Katuscak and Ozdenoren (2005, 2009).
Quenching of Tryptophan Fluorescence in the Presence of 2,4-DNP, 2,6-DNP, 2,4-DNA and DNOC and Their Mechanism of Toxicity

Although they are widely used as insecticides, acaricides and fungicides in the agriculture or as raw materials in the dye industry, dinitrophenols (DNPs) are extremely noxious, death cases having been registered. These compounds produce cataracts, lower leucocyte levels, disturb the general metabolism and can cause cancer. It is also assumed that DNPs hinder the proton translocation through the mitochondrial inner membrane and therefore inhibit oxidative phosphorylation. Their fluorescence quenching properties can help understand and explain their toxicity. Fluorescence quenching of tryptophan was tested using different dinitrophenols such as 2,4-dinitrophenol (2,4-DNP), 4,6-dinitro-orthocresol (DNOC), 2-[(2,4-dinitrophenyl)amino]acetic acid (GlyDNP), 2-(1-methyl-heptyl)-4.6-dinitrophenyl crotonate (Karathan), 2-amino-5-[(1-((carboxymethyl)amino)-3-((2,4-dinitrophenyl)thio)-1-oxopropan-2-yl)amino]-5-oxopentanoic acid (SDN GSH), 2,4-dinitroanisole (2,4-DNA) and 2,4-dinitrobenzoic acid (2,4-DNB). 2,4-DNP and DNOC showed the highest tryptophan fluorescence quenching constant values, these being also the most toxic compounds. The electronic chemical potential value of the most stable complex of 2,4-DNP-with tryptophan is higher than the values of the electronic chemical potentials of complexes corresponding to the derivatives.
A Discriminative Hierarchical Model for Fast Coreference at Large Scale

Methods that measure compatibility between mention pairs are currently the dominant approach to coreference. However, they suffer from a number of drawbacks including difficulties scaling to large numbers of mentions and limited representational power. As these drawbacks become increasingly restrictive, the need to replace the pairwise approaches with a more expressive, highly scalable alternative is becoming urgent. In this paper we propose a novel discriminative hierarchical model that recursively partitions entities into trees of latent sub-entities. These trees succinctly summarize the mentions providing a highly compact, information-rich structure for reasoning about entities and coreference uncertainty at massive scales. We demonstrate that the hierarchical model is several orders of magnitude faster than pairwise, allowing us to perform coreference on six million author mentions in under four hours on a single CPU.
Evaluating observers' sensitivity to errors in human and physical throws

Understanding whether observers are sensitive to physical distortions in dynamic events is important in order to develop plausible simulations while saving time on details that observers cannot perceive [Barzel et al. 1996]. In this experiment, we evaluated observers' sensitivity to physical distortions in virtual throwing animations. As previous results showed a greater sensitivity to physical distortions on virtual human characters rather than on simple objects [Reitsma et al. 2008], we studied the effect of using both a biological human throw and a simple physical simulation (free fall of a ball on a ramp). The results show that observers' sensitivity to errors depends on the animacy of the thrower.
Open access - Research article THIS ARTICLE IS PART OF A SPECIAL ISSUE ENTITLED 'FLOODING STRESS' Regression analysis of growth responses to water depth in three wetland plant species

Background and aims Plant species composition in wetlands and on lakeshores often shows dramatic zonation, which is frequently ascribed to differences in flooding tolerance. This study compared the growth responses to water depth of three species (Phormium tenax, Carex secta and Typha orientalis) differing in depth preferences in wetlands, using non-linear and quantile regression analyses to establish how flooding tolerance can explain field zonation. Methodology Plants were established for 8 months in outdoor cultures in waterlogged soil without standing water, and then randomly allocated to water depths from 0 to 0.5 m. Morphological and growth responses to depth were followed for 54 days before harvest, and then analysed by repeated-measures analysis of covariance, and non-linear and quantile regression analysis (QRA), to compare flooding tolerances. Principal results Growth responses to depth differed between the three species, and were non-linear. Phormium tenax growth decreased rapidly in standing water . 0.25 m depth, C. secta growth increased initially with depth but then decreased at depths . 0.30 m, accompanied by increased shoot height and decreased shoot density, and T. orientalis was unaffected by the 0- to 0.50-m depth range. In P. tenax the decrease in growth was associated with a decrease in the number of leaves produced per ramet and in C. secta the effect of water depth was greatest for the tallest shoots. Allocation patterns were unaffected by depth. Conclusions The responses are consistent with the principle that zonation in the field is primarily structured by competition in shallow water and by physiological flooding tolerance in deep water. Regression analyses, especially QRA, proved to be powerful tools in distinguishing genuine phenotypic responses to water depth from non-phenotypic variation due to size and developmental differences.
Is species richness driving intra- and interspecific interactions and temporal activity overlap of a hantavirus host? An experimental test

High species diversity of the potential animal host community for a zoonotic pathogen may reduce pathogen transmission among the most competent host, a phenomenon called the “dilution effect”, but the mechanisms driving this effect have been little studied. One proposed mechanism is “encounter reduction” where host species of low-competency decrease contact rates between infected and susceptible competent hosts, especially in directly transmitted diseases. We conducted an experiment in outdoor enclosures in northwestern Mexico where we manipulated rodent assemblages to assess the effect of species richness on the frequency of intra- and interspecific interactions and activity patterns of a hantavirus reservoir host (North American deermouse; Peromyscus maniculatus). Trials consisted of three treatments of rodent assemblages that differed in species richness, but had equal abundance of deermice; treatment 1 consisted of only deermice, treatment 2 included deermice and one non-competent host species, and treatment 3 included two non-competent host species in addition to deermice. To measure interactions and temporal activity, we strategically deployed foraging stations and infrared cameras. We did not find differences in the frequency of intraspecific interactions of deermice among treatments, but there were significantly more interspecific interactions between deermouse and non-competent hosts in treatment 2 than treatment 3, which is explained by the identity of the non-competent host species. In addition, there were differences in activity patterns between rodent species, and also between deermice from treatment 1 and treatment 2. These results indicate that at least at a small-scale analysis, the co-occurrence with other species in the study area does not influence the frequency of intraspecific interactions of deermice, and that deermice may be changing their activity patterns to avoid a particular non-competent host species (Dipodomys merriami). In conclusion, in this deermouse-hantavirus system a potential dilution effect would not be through intraspecific encounter reduction in the most competent hantavirus host. To identify variables of host assemblages that can influence pathogen transmission, we highlight the need to address the identity of species and the composition of assemblages, not only host species richness or diversity.
Ferroelectric switching characteristics of 73/27 copolymer of vinylidene fluoride and trifluoroethylene

Ferroelectric polarization-reversal switching of vinylidene fluoride—trifluoroethylene copolymer with 73 mol % of vinylidene fluoride is investigated under a variety of conditions in an attempt to derive detailed information on the polarization reversal of the polymer. The electric-field dependence of switching time ts obeys an exponential law. The temporal change of switching current density J is presented in the form J/(Ps − P) versus time (P is the polarization, and Ps is its saturation value), which is free of the depolarization-field effect and discriminates in a straightforward manner between acceleration and deceleration of switching. Effects of the annealing of samples upon ts are observed together with changes in the degree of crystallinity. Effects of space charge distribution upon ts are investigated by applying two successive pulses, positive and negative, with varied intervals tw between the two. The dynamics of space charge redistribution is elucidated from the tw dependence of the ts of the second pulse. The temperature dependence of ts indicates that the switching becomes critically fast as the phase-transition temperature is approached.
VENOUS THROMBOEMBOLISM IN THAI CHILDREN

This is a retrospective study of 24 pediatric venous thromboembolism (VTE) patients with or without pulmonary embolism, conducted in Bangkok, Thailand, between 1981 and 2005. The incidence rate of VTE in Thai children was 3.9/10,000 hospital admissions per year. The median age was 11.7 years. Seventy-five percent of the patients had at least one associated medical condition accounting for the VTE; the two most common conditions, however, were infection and malignancy. Pulmonary embolism occurred in 29% of patients. Observed outcomes of VTE in this series included death (13%), postphlebitic syndrome (13%), and recurrence (26%). Genetic risk factors were explored in 19 patients, and no factor V Leiden or prothrombin 20210 mutations were detected. Protein C deficiency was found in 4 patients.
Deep convolutional neural networks for interpretable analysis of EEG sleep stage scoring

Sleep studies are important for diagnosing sleep disorders such as insomnia, narcolepsy or sleep apnea. They rely on manual scoring of sleep stages from raw polisomnography signals, which is a tedious visual task requiring the workload of highly trained professionals. Consequently, research efforts to purse for an automatic stage scoring based on machine learning techniques have been carried out over the last years. In this work, we resort to multitaper spectral analysis to create visually interpretable images of sleep patterns from EEG signals as inputs to a deep convolutional network trained to solve visual recognition tasks. As a working example of transfer learning, a system able to accurately classify sleep stages in new unseen patients is presented. Evaluations in a widely-used publicly available dataset favourably compare to state-of-the-art results, while providing a framework for visual interpretation of outcomes.
Magnetic Determination of the Relationship between the S‐T Segment Shift and the Injury Current Produced by Coronary Artery Occlusion

Both the S-T segment shift and the injury current were measured using the direct-current magnetocardiogram (d-c MCG) in seven dogs undergoing coronary artery occlusion. The purpose of the measurements was to clarify the origin of the S-T shift in acute ischemia and infarction. Previous measurements, consisting of d-c electrograms recorded from the exposed epicardial surface in situ, are partially inconsistent; also, they are not necessarily representative of the surface electrocardiogram (ECG), which sums broadly over the myocardium. The d-c MCG allows steady myocardial currents in the intact torso to be measured externally; because the d-c MCG sums broadly over these currents, conclusions drawn from it are applicable to the ECG. Coronary artery occlusion was produced by inflating a tube which, about 1 week earlier, had been surgically installed around the artery and exteriorized. During occlusions carried out in the MIT magnetically shielded room, a sensitive magnetometer recorded the d-c MCG at various locations around the torso. Within 20 seconds after occlusion, equal and opposite S-T segment and base-line (d-c) shifts appeared on the d-c MCG; these shifts were maintained for at least 15 minutes, after which they slowly decreased. Therefore, during the acute ischemia produced by these occlusions, the S-T shift is a secondary result of a primary injury current that is interrupted during the S-T interval.
Analysis of cyt0kine gene expression in stimulated T cells of small children by semi-quantitative PCR

Only limited amounts of peripheral blood samples can be obtained from small children. Therefore, a polymerase chain reaction (PCR) aided analysis of cytokine gene expression by PBMC or T cells is a valuable tool. We present a combination of procedures to obtain an accurate estimation of the expression of the cytokines IL-4 and IFN-γ. This can be performed on T cells purified from blood samples of up to 5 ml in volume from children aged 0–4 years with allergic asthma and atopic dermatitis. This procedure includes multiple sampling of PCR products to determine the linear phase of the PCR; inter-experiment correction using a helper T-cell clone, expressing both IL-4 and IFN-γ; interpatient correction by comparing the expression of a housekeeping gene (HPRT); and finally the development of specific software to analyse densitometric data obtained by scanning photographs of agarose gels, separating PCR products. In this way it is possible to study cytokine gene expression from a very small amount of material.
Ferredoxin:NADPH oxidoreductase is recruited to thylakoids by binding to a polyproline type II helix in a pH-dependent manner

Ferredoxin:NADPH oxidoreductase (FNR) is a key enzyme of photosynthetic electron transport required for generation of reduction equivalents. Recently, two proteins were found to be involved in membrane-anchoring of FNR by specific interaction via a conserved Ser/Pro-rich motif: Tic62 and Trol. Our crystallographic study reveals that the FNR-binding motif, which forms a polyproline type II helix, induces self-assembly of two FNR monomers into a back-to-back dimer. Because binding occurs opposite to the FNR active sites, its activity is not affected by the interaction. Surface plasmon resonance analyses disclose a high affinity of FNR to the binding motif, which is strongly increased under acidic conditions. The pH of the chloroplast stroma changes dependent on the light conditions from neutral to slightly acidic in complete darkness or to alkaline at saturating light conditions. Recruiting of FNR to the thylakoids could therefore represent a regulatory mechanism to adapt FNR availability/activity to photosynthetic electron flow.