Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental Factors Influencing Epidemic Cholera

Letter to the Editor Environmental Factors Influencing Epidemic Cholera Dear Sir: We have concerns with the recent publication by Jutla and colleagues, which aims to describe the environmental factors influencing epidemic cholera. 1 Regarding cholera in Haiti, the authors challenged the findings of many studies showing that the epidemic likely originated from the importation of toxi-genic Vibrio cholerae by Nepalese peacekeepers in October 2010. 2–5 Instead, they attempted to show that environmental conditions conducive to rapid growth and transmission of V. cholerae played a substantial role in epidemic onset. Their hypothesis is based on the claim that increased temperatures and rainfall during the months preceding the epidemic favored the proliferation of V. cholerae in the Haitian waters and its subsequent transmission to the local population 1 ; we believe their claims are based on misinterpretations of our published data and statistical correlations that fail to establish causality. Our field investigation of the Haitian cholera epidemic has clearly indicated that outbreaks started in Meye, near Mirebalais, before subsequently spreading downstream, following the Artibonite River. 2 Using a Spearman's rank statistical test, Jutla and colleagues stated that the correlation between cholera cases in Mirebalais and the Lower Artibonite was " very high, " thereby inferring that the epidemic started simultaneously in the two locations. 1 According to our report, each of the Lower Artibonite communes displayed a markedly higher correlation with the other Lower Artibonite communes than with Mirebalais. 2 Therefore, we did not report a strong correlation between Mirebalais and the Lower Artibonite communes , as claimed by Jutla and colleagues. 1 Nevertheless, correlation analyses are irrelevant to question the chronological progression of the epidemic. Indeed, our field investigation revealed that no suspected cases of cholera or severe diarrhea were reported in the Lower Artibonite before October 19, although the epidemic began on October 14 near Mirebalais. 2
An Ad-Hoc Initial Solution Heuristic for Metaheuristic Optimization of Energy Market Participation Portfolios

The deregulation of the electricity sector has culminated in the introduction of competitive markets. In addition, the emergence of new forms of electric energy production, namely the production of renewable energy, has brought additional changes in electricity market operation. Renewable energy has significant advantages, but at the cost of an intermittent character. The generation variability adds new challenges for negotiating players, as they have to deal with a new level of uncertainty. In order to assist players in their decisions, decision support tools enabling assisting players in their negotiations are crucial. Artificial intelligence techniques play an important role in this decision support, as they can provide valuable results in rather small execution times, namely regarding the problem of optimizing the electricity markets participation portfolio. This paper proposes a heuristic method that provides an initial solution that allows metaheuristic techniques to improve their results through a good initialization of the optimization process. Results show that by using the proposed heuristic, multiple metaheuristic optimization methods are able to improve their solutions in a faster execution time, thus providing a valuable contribution for players support in energy markets negotiations.
AIF and Scythe (Bat3) Regulate Phosphatidylserine Exposure and Macrophage Clearance of Cells Undergoing Fas (APO-1)-Mediated Apoptosis

Phosphatidylserine (PS) exposure on the cell surface has been considered a characteristic feature of apoptosis and serves as a molecular cue for engulfment of dying cells by phagocytes. However, the mechanism of PS exposure is still not fully elucidated. Here we show that the cytosolic release from mitochondria of apoptosis-inducing factor (AIF) is required for PS exposure during death receptor-induced apoptosis and for efficient clearance of cell corpses by primary human macrophages. Fas-triggered PS exposure was significantly reduced upon siRNA-mediated silencing of AIF expression and by inhibition of the cytosolic translocation of AIF. In addition, AIF localizes to the plasma membrane upon Fas ligation and promotes activation of phospholipid scrambling activity. Finally, cytosolic stabilization of AIF through interaction with Scythe is shown to be involved in apoptotic PS exposure. Taken together, our results suggest an essential role for AIF and its binding partner Scythe in the pathway leading to apoptotic corpse clearance.
Impact of Circulating Cholesterol Levels on Growth and Intratumoral Androgen Concentration of Prostate Tumors

Prostate cancer (PCa) is the second most common cancer in men. Androgen deprivation therapy (ADT) leads to tumor involution and reduction of tumor burden. However, tumors eventually reemerge that have overcome the absence of gonadal androgens, termed castration resistant PCa (CRPC). Theories underlying the development of CRPC include androgen receptor (AR) mutation allowing for promiscuous activation by non-androgens, AR amplification and overexpression leading to hypersensitivity to low androgen levels, and/or tumoral uptake and conversion of adrenally derived androgens. More recently it has been proposed that prostate tumor cells synthesize their own androgens through de novo steroidogenesis, which involves the step-wise synthesis of androgens from cholesterol. Using the in vivo LNCaP PCa xenograft model, previous data from our group demonstrated that a hypercholesterolemia diet potentiates prostatic tumor growth via induction of angiogenesis. Using this same model we now demonstrate that circulating cholesterol levels are significantly associated with tumor size (R = 0.3957, p = 0.0049) and intratumoral levels of testosterone (R = 0.41, p = 0.0023) in LNCaP tumors grown in hormonally intact mice. We demonstrate tumoral expression of cholesterol uptake genes as well as the spectrum of steroidogenic enzymes necessary for androgen biosynthesis from cholesterol. Moreover, we show that circulating cholesterol levels are directly correlated with tumoral expression of CYP17A, the critical enzyme required for de novo synthesis of androgens from cholesterol (R = 0.4073, p = 0.025) Since hypercholesterolemia does not raise circulating androgen levels and the adrenal gland of the mouse synthesizes minimal androgens, this study provides evidence that hypercholesterolemia increases intratumoral de novo steroidogenesis. Our results are consistent with the hypothesis that cholesterol-fueled intratumoral androgen synthesis may accelerate the growth of prostate tumors, and suggest that treatment of CRPC may be optimized by inclusion of cholesterol reduction therapies in conjunction with therapies targeting androgen synthesis and the AR.
Fine root architecture, morphology, and biomass response to cutting in a Chinese cork oak (Quercus variabilis Blume) forest

This study aims to detect the variety of fine root growth with branch orders in response to forest cutting. The branching ratio (Rb), root morphological indices, and biomass of up to 3 branch orders of fine roots were investigated from 2 soil depths (0 cm to 10 cm and 10 cm to 20 cm) in Chinese cork oak (Quercus variabilis Blume) plots 1 and 3 years after forest cutting, compared with those of intact trees as the control. The number of fine roots was lower in the managed plots than in the control, particularly in the first-order roots. After 1 year of cutting, the proportion of the first-order roots decreased significantly, whereas the proportion of the second-order and third-order roots increased. Rb decreased significantly after forest management in the 0-10 cm soil depth of plots after 1 year of cutting. The fine roots in the plots after cutting exhibited less root length density, lower specific root length, less surface area, and higher tissue density compared with those in control plots. The mean root diameter showed no significant change. The average biomass of the first 3 orders of roots in the plots 1 and 3 years after cutting was 72% and 83% of that of the control plot, respectively. The reduction of fine root growth was influenced mainly by the lack of photosynthesis in the managed forest.
Searching for Glycosylated Natural Products in Actinomycetes and Identification of Novel Macrolactams and Angucyclines

Many bioactive natural products are glycosylated compounds in which the sugar components usually participate in interaction and molecular recognition of the cellular target. Therefore, the presence of sugar moieties is important, in some cases essential, for bioactivity. Searching for novel glycosylated bioactive compounds is an important aim in the field of the research for natural products from actinomycetes. A great majority of these sugar moieties belong to the 6-deoxyhexoses and share two common biosynthetic steps catalyzed by a NDP-D-glucose synthase (GS) and a NDP-D-glucose 4,6-dehydratase (DH). Based on this fact, seventy one Streptomyces strains isolated from the integument of ants of the Tribe Attini were screened for the presence of biosynthetic gene clusters (BGCs) for glycosylated compounds. Total DNAs were analyzed by PCR amplification using oligo primers for GSs and DHs and also for a NDP-D-glucose-2,3-dehydratases. Amplicons were used in gene disruption experiments to generate non-producing mutants in the corresponding clusters. Eleven mutants were obtained and comparative dereplication analyses between the wild type strains and the corresponding mutants allowed in some cases the identification of the compound coded by the corresponding cluster (lobophorins, vicenistatin, chromomycins and benzanthrins) and that of two novel macrolactams (sipanmycin A and B). Several strains did not show UPLC differential peaks between the wild type strain and mutant profiles. However, after genome sequencing of these strains, the activation of the expression of two clusters was achieved by using nutritional and genetic approaches leading to the identification of compounds of the cervimycins family and two novel members of the warkmycins family. Our work defines a useful strategy for the identification new glycosylated compounds by a combination of genome mining, gene inactivation experiments and the activation of silent biosynthetic clusters in Streptomyces strains.
Relationship between arterial pressure and pulse wave velocity using photoplethysmography during the post-exercise recovery period

Blood pressure is an important parameter for health assessment. Noninvasive continuous beat per beat blood pressure measurement is still a complicated and expensive procedure. There is a lack of agreement on the optimal blood pressure measurement technique. Potentially the most useful indirect parameter for blood pressure monitoring could be pulse wave velocity or the inverse – pulse transit time. The objectives of the study was to determine the relationship between blood pressure and pulse wave velocity under conditions when different cardiovascular parameters change independently but simultaneously with blood pressure and to clarify whether there is a difference in relationship between blood pressure and pulse wave velocity measured by two different methods in different vascular beds. We determined the relationship between arterial blood pressure (systolic, mean) and the pulse wave velocity from 20 healthy volunteers during a post-exercise recovery period after a load cycling test. A significant correlation (p < 0.05) and regression (p < 0.001) between arterial pressure and pulse wave velocity was obtained. Pulse wave velocity measurement measured in different vascular beds showed no impact on correlation of arterial blood pressure and pulse wave velocity. The average difference between measured and calculated arterial blood pressure values did not exceed 10 mm Hg.
What a Coincidence! The Effects of Incidental Similarity on Compliance

Four studies examined the effect of an incidental similarity on compliance to a request. Undergraduates who believed they shared a birthday (Study 1), a first name (Study 2), or fingerprint similarities (Study 3) with a requester were more likely to comply with a request than participants who did not perceive an incidental similarity with the requester. The findings are consistent with past research demonstrating that people often rely on heuristic processing when responding to requests and with Heider’s description of unit relationships in which perceived similarities lead to positive affect. Consistent with the unit relation interpretation, participants did not increase compliance when hearing about an incidental similarity with someone other than the requester or when they believed the feature they shared with the requester was common.
Nonparametric Small Area Estimation Using Penalized Spline Regression

We propose a new small area estimation approach that combines small area random effects with a smooth, nonparametrically specified trend. By using penalized splines as the representation for the nonparametric trend, it is possible to express the small area estimation problem as a mixed effect model regression. This model is readily fitted using existing model fitting approaches such as restricted maximum likelihood. We develop a corresponding bootstrap approach for model inference and estimation of the small area prediction mean squared error. The applicability of the method is demonstrated on a survey of lakes in the Northeastern US.
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

Summary: Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes. Availability and implementation: Code in Python is at http://bioinform.github. io/metasv/. Contact: rd@bina.com Supplementary information: Supplementary data are available at Bioinformatics online.
Investigation of the coarse grained heat-affected zone microstructure and hardness of multipass welded X65 linepipe steel.

In this thesis the effect of single and multipass welding on the microstructure and hardness of X65 linepipe steel of four different chemical compositions was investigated. The welding was simulated for three different heat inputs and two second pass peak temperatures. The thermal simulation has been achieved by simulating the CGHAZ with a Gleeble? thermal-mechanical simulator, peak temperatures used for this simulation were derived from dilatometer experiments. Significant overheating of 50 ? C above Ac1 was observed at high heating rates, comparable heating rates of welding. The peak temperature of the first weld cycle was 1350 ? C and the second cycle either 810 ? C or 860 ? C. The overall hardness of the samples was measured as was the micro hardness of M-A constituents. The microhardness of M-A constituents was found to be significantly lower than in previous research, 310 Hv versus 800 Hv. The hardness of the single pass CGHAZ was parametrized for the cooling rate and the chemical composition with an R2 value 0.98. The parametrization shows increased hardenability due to increased Ni content. The CGHAZ microstructures were examined by optical and scanning electron microscopy as well as EBSD, revealing microstructures consisting of martensite, lower bainite, upper bainite, granular bainite, acicular ferrite and M-A constituents. A number of samples were quantitatively described by use of the IQ distribution from EBSD measurements and the M-A constituents were quantified by Lepera’s etchant for all multipass welded samples. A fraction of M-A constituents was found to be higher than 1.6 %all reheated CGHAZ samples and the fraction is found to be dependent on the heat input and hardenability of the steel. It was found that Lepera’s etchant reveals a higher fraction of M-A constituents than what is observed by EBSD measurements. The M-A constituents as revealed by Lepera’s etchant were found to not completely consist martensite and austenite in the steels considered in this research. Therefore the M-A constituents are suspected to be of less importance for the fracture toughness than discussed in previous research.
Repeated Measurement of the Components of Attention of Older Adults using the Two Versions of the Attention Network Test: Stability, Isolability, Robustness, and Reliability

Ishigami and Klein (2010) showed that scores of the three attention networks (alerting, orienting, and executive control) measured with the two versions of the Attention Network Test (ANT; Fan et al., 2002; Callejas et al., 2005) were robust over 10 sessions of repeated testing even though practice effects were consistently observed especially in the executive network when young adults were tested. The current study replicated their method to examine robustness, stability, reliability, and isolability of the networks scores when older adults were tested with these ANTs. Ten test sessions, each containing two versions of the ANT, were administered to 10 older adults. Participants were asked to indicate the direction of a target arrow, flanked by distractors, presented either above or below the fixation following auditory signals or/and visual cue. Network scores were calculated using orthogonal subtractions of performance in selected conditions. All network scores remained highly significant even after nine previous sessions despite some practice effects in the executive and the alerting networks. Some lack of independence among the networks was found. The relatively poor reliability of network scores with one session of data rises to respectable levels as more data is added.
Targeting delivery of anti-TNFα oligonucleotide into activated colonic macrophages protects against experimental colitis

Background and aims Tumour necrosis factor α (TNFα) is a focal point of the inflammatory cascade in Crohn's disease (CD). As an emerging approach to block cytokines, antisense oligonucleotide (ASO) has developed quickly, but is thwarted by a key obstacle—safe and effective delivery to specified cells. Here a novel nano-complex, based on galactosylated low molecular weight chitosan (gal-LMWC) and an ASO against TNFα, is presented which may be effective for CD treatment. The aim of this study was to investigate the targeting delivery ability of the gal-LMWC/ASO complex into activated macrophages and its potential therapeutic action in experimental colitis. Methods Gal-LMWC was associated with ASO to form a stable nano-complex and the complex was injected into mice by intracolonic administration. Cellular localisation of the gal-LMWC/ASO complex in the colon was determined. The therapeutic effects were further studied in 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis and CD4+CD45RBhi T cell transfer colitis. Results Intracolonic administration of the gal-LMWC/ASO complex resulted in the successful delivery of ASO into activated colonic macrophages and a significant reduction of colonic TNFα in mice with colitis. A single injection in TNBS colitis or repeated treatment in CD45RBhi transfer colitis both significantly ameliorated the clinical and histopathological severity of the wasting disease, reduced tissue levels of inflammatory cytokines and abrogated body weight loss, diarrhoea and intestinal protein loss. Conclusions It is the first time a non-viral gene vector has been combined with an ASO targeted to activated macrophages in the treatment of CD. The inhibition of TNFα by this strategy represents a promising therapeutic approach for the treatment of CD.
A-tract clusters may facilitate DNA packaging in bacterial nucleoid

Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816–3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed ‘quasi-regularly’ throughout the genome, including both the coding and intergenic sequences. Second, there is a 10–12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in ∼100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the ∼100 bp long clusters of the phased A-tracts constitute the ‘structural code’ for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins.
Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication

The basic leucine zipper (bZIP) transcription factors are the most diverse members of dimerizing transcription factors. In the present study, 50, 116, and 47 bZIP genes were identified in Malus domestica (apple), Prunus persica (peach), and Fragaria vesca (strawberry), respectively. Species-specific duplication was the main contributor to the large number of bZIPs observed in apple. After WGD in apple genome, orthologous bZIP genes corresponding to strawberry on duplicated regions in apple genome were retained. However, in peach ancestor, these syntenic regions were quickly lost or deleted. Maybe the positive selection contributed to the expansion of clade S to adapt to the development and environment stresses. In addition, purifying selection was mainly responsible for bZIP sequence-specific DNA binding. The analysis of orthologous pairs between chromosomes indicates that these orthologs derived from one gene duplication located on one of the nine ancient chromosomes in the Rosaceae. The comparative analysis of bZIP genes in three species provides information on the evolutionary fate of bZIP genes in apple and peach after they diverged from strawberry.