Miracle-dz/UniFAR-FTUs huggingface dataset:
Noninvasive molecular and morphological evidences for an undiscovered population of snow vole in Southern Spain

Capturing wild animals can be time consuming and difficult or even impractical. Noninvasive sampling is potentially a cost-effective and efficient means to monitor wild animals, thereby avoiding the need of capture and disturb species in the wild. On the basis of the morphological and genetic analyses of owl pellet contents, a so far undetected European snow vole (Chionomys nivalis) population was discovered in the Sierra Segura mountain range (Southern Spain). The mtDNA sequence from the newly discovered haplotype was compared with sequences from vole populations of the Sierra Nevada and Sierra Peñalara mountain ranges (Spain) and from Churwalden (Switzerland). The nine recovered haplotypes clustered in four distinct lineages according to their geographical origin. The vole sequence from the Sierra Segura owl pellet belonged to a new haplotype, constituting a new lineage. The evolutionary divergence between sequences from the Sierra Segura and other Spanish populations was higher than that among other Spanish haplotypes. The new snow vole haplotype from this new locality duplicates the number of occurrence sites of this critically endangered species in Southern Spain, which is of great interest for further conservation and management plans of the European snow vole in the most southwestern area of its entire distribution range.
A new modeling approach for quantifying expert opinion in the drug discovery process

Expert opinion plays an important role when choosing clusters of chemical compounds for further investigation. Often, the process by which the clusters are assigned to the experts for evaluation, the so‐called selection process, and the qualitative ratings given by the experts to the clusters (chosen/not chosen) need to be jointly modeled to avoid bias. This approach is referred to as the joint modeling approach. However, misspecifying the selection model may impact the estimation and inferences on parameters in the rating model, which are of most scientific interest. We propose to incorporate the selection process into the analysis by adding a new set of random effects to the rating model and, in this way, avoid the need to model it parametrically. This approach is referred to as the combined model approach. Through simulations, the performance of the combined and joint models was compared in terms of bias and confidence interval coverage. The estimates from the combined model were nearly unbiased, and the derived confidence intervals had coverage probability around 95% in all scenarios considered. In contrast, the estimates from the joint model were severely biased under some form of misspecification of the selection model, and fitting the model was often numerically challenging. The results show that the combined model may offer a safer alternative on which to base inferences when there are doubts about the validity of the selection model. Importantly, thanks to its greater numerical stability, the combined model may outperform the joint model even when the latter is correctly specified. Copyright © 2015 John Wiley & Sons, Ltd.
On the Role of Neurogenesis and Neural Plasticity in the Evolution of Animal Personalities and Stress Coping Styles

Individual variation in how animals react to stress and environmental change has become a central topic in a wide range of biological disciplines, from evolutionary ecology to biomedicine. Such variation manifests phenotypically as correlated trait-clusters (referred to as coping styles, behavioral syndromes, shyness-boldness, or personality traits). Thresholds for switching from active coping (fight-flight) to inhibition and passive behavior when exposed to stress depend on experience and genetic factors. Comparative research has revealed a range of neuroendocrine-behavioral associations which are conserved throughout the vertebrate subphylum, including factors affecting perception, learning, and memory of stimuli and events. Here we review conserved aspects of the contribution of neurogenesis and other aspects of neural plasticity to stress coping. In teleost fish, brain cell proliferation and neurogenesis have received recent attention. This work reveals that brain cell proliferation and neurogenesis are associated with heritable variation in stress coping style, and they are also differentially affected by short- and long-term stress in a biphasic manner. Routine-dependent and inflexible behavior in proactive individuals is associated with limited neural plasticity. These evolutionarily conserved relationships hold the potential to illuminate the biological background for stress-related neurobiological disorders.
Improved photocurrent in Cu(In,Ga)Se2 solar cells: From 20.8% to 21.7% efficiency

New processing developments in the Cu(In,Ga)Se2 (CIGS)-based solar cell technology have enabled progress to the next level of best cell efficiencies exceeding 21%. This result was achieved by applying the alkali post-deposition treatment (PDT) to the CIGS film, which effects changes both in the bulk and on the surface of the film. Furthermore, we have found that these modifications affect the range of optimal CIGS growth parameters and the minimal thickness of the CdS buffer layer. Our first experiences with PDT lead to a 20.8% record device. Later optimizations in the composition profile and CdS buffer layer thickness enabled us to increase the photocurrent density with only a slight loss in open-circuit voltage and unchanged fill factor, resulting in the current world record of 21.7% efficiency. This contribution presents measurements, simulations, and a discussion of the photocurrent increase.
multi‐dice: r package for comparative population genomic inference under hierarchical co‐demographic models of independent single‐population size changes

Population genetic data from multiple taxa can address comparative phylogeographic questions about community‐scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co‐demographic models that directly test multi‐taxa hypotheses within a single, unified analysis. This approach has been applied to classical phylogeographic data sets such as mitochondrial barcodes as well as reduced‐genome polymorphism data sets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD‐seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest and composite likelihood optimization. Here, we introduce the r package multi‐dice, a wrapper program that exploits existing simulation software for flexible execution of hierarchical model‐based inference using the aSFS, which is derived from reduced genome data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding co‐demographic pulses and specifying flexible hyperprior distributions. In sum, multi‐dice provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a tool for comparative phylogeography and population genomics.
The Influence of Viewing Photos of Different Types of Rural Landscapes on Stress in Beijing

The environment can affect people’s health by relieving stress, and rural landscape as a special environment might influence human’s stress relief. This study takes different types of rural landscapes as the research object to explore their impact on stress levels, which are shown by photos. As an independent variable, the rural landscape is divided into three levels: Type 1 (natural landscape), type 2 (productive landscape), and type 3 (artificial landscape). Seventy-three subjects were randomly assigned to each type of rural landscape. Salivary cortisol, blood pressure, heart rate, and a subjective rating state scale (brief profile of mood states, BPOMS) were used as indicators of stress. At the same time, the influence of preference and familiarity on the stress relieving effect was also discussed. A paired t-test and one-way analysis of variance (ANOVA) were used as the main statistical methods. In the results of t-test for pre-posttest, significant difference was observed in high blood pressure, heart rate, and total mood disturbance (TMD) of type 1 and type 2, and the high and low blood pressure of type 3; ANOVA analysis revealed that for the difference of pre-posttest, significant difference was observed in the TMD value among the three types; except for type 3, blood pressure, heart rate, and BPOMS values were significantly affected by preference and familiarity. The conclusions include the following: The three types of rural landscapes have a positive effect on relieving stress; the productive landscape has the best effect on relieving stress; and users’ landscape preferences and familiarity with the environment can affect the effect of stress relief in rural landscapes.
An evaluation of the measurement of the activities of complexes I-IV in the respiratory chain of human skeletal muscle mitochondria.

The measurement of individual respiratory chain complexes is an important component of the investigation of diseases due to mitochondrial dysfunction. We have evaluated assays which measure complexes I to IV in human skeletal muscle mitochondria and in addition optimized these assays to provide sensitive and reliable diagnostic techniques, particularly in situations where a partial interruption at a single complex needs to identified. Using several established methods of membrane disruption we have found that optimal activities of complexes I and II are obtained by freeze-thawing the mitochondria in hypotonic potassium phosphate buffer, whereas complex III and IV activities are markedly increased by the addition of the detergent n-dodecyl-beta-D-maltoside. Complex I activity is measured in the presence of 2.5 mg.ml-1 bovine serum albumin, which increases rotenone sensitivity, and we have shown that NADH-cytochrome b5 reductase makes an important contribution to the rotenone-insensitive NADH-ubiquinone oxidoreductase activity. Complex II activity is measured after preincubation of the mitochondrial fraction with succinate to fully activate the complex. Complex I and III activities are dependent upon the length of the isoprenoid chain of the ubiquinone and ubiquinol, respectively. These assays have been used to establish a control range.
Reversible labeling of cysteine‐containing peptides allows their specific chromatographic isolation for non‐gel proteome studies

We report upon a novel procedure to specifically isolate cysteine‐containing peptides from a complex peptide mixture. Cysteines are converted to hydrophobic residues by mixed disulfide formation with Ellman's reagent. Proteins are subsequently digested with trypsin and the generated peptide mixture is a first time fractionated by reverse‐phase high‐performance liquid chromatography. Cysteinyl‐peptides are isolated out of each primary fraction by a reduction step followed by a secondary peptide separation on the same column, performed under identical conditions as for the primary separation. The reducing agent removes the covalently attached group from the cysteine side chain, making cysteine‐peptides more hydrophilic and, thereby, such peptides can be specifically collected during the secondary separation and are finally used to identify their precursor proteins using automated liquid chromatography tandem mass spectrometry. We show that this procedure efficiently isolates cysteine‐peptides, making the sample mixture less complex for further analysis. This method was applied for the analysis of the proteomes of human platelets and enriched human plasma. In both proteomes, a significant number of low abundance proteins were identified next to extremely abundant ones. A dynamic range for protein identification spanning 4–5 orders of magnitude is demonstrated.
A randomized double-blind crossover trial of deep brain stimulation of the subcallosal cingulate gyrus in patients with treatment-resistant depression: a pilot study of relapse prevention.

BACKGROUND To date, antidepressant drugs show limited efficacy, leaving a large number of patients experiencing severe and persistent symptoms of major depression. Previous open-label clinical trials have reported significant sustained improvements with deep brain stimulation (DBS) of the subcallosal cingulate gyrus (SCG) in patients with severe, chronic treatment-resistant depression (TRD). This study aimed to confirm the efficacy and measure the impact of discontinuation of the electrical stimulation. METHODS We conducted a 6-month double-blind, randomized, sham-controlled crossover study in implanted patients with previous severe TRD who experienced full remission after chronic stimulation. After more than 3 months of stable remission, patients were randomly assigned to 2 treatment arms: the ON-OFF arm, which involved active electrode stimulation for 3 months followed by sham stimulation for 3 months, and the OFF-ON arm, which involved sham stimulation for 3 months followed by active stimulation for 3 months. The primary outcome measure was the difference in the 17-item Hamilton Rating Scale for Depression (HAMD-17) total score between sham and active stimulation. RESULTS We enrolled 5 patients in our trial. A Friedman repeated-measures analysis of variance revealed a significant effect of treatment (χ(2)1 = 5.0, p = 0.025) in patients with higher depression scores during sham stimulation. At the end of active stimulation, depression was remitted in 4 of 5 patients and none of them had experienced a relapse, whereas at the end of sham stimulation, 2 patients remained in remission, 2 relapsed and 1 showed a progressive worsening without reaching relapse criteria. LIMITATIONS The small sample size limited the statistical power and external validity. CONCLUSION These preliminary findings indicate that DBS of the SCG is an effective and safe treatment for severe forms of TRD and that continuous electrical stimulation is required to maintain therapeutic effects. TRIAL REGISTRATION NCT01268137 (ClinicalTrials.gov).
Multiple DNA Damage Signaling and Repair Pathways Deregulated by Simian Virus 40 Large T Antigen

ABSTRACT We demonstrated previously that expression of simian virus 40 (SV40) large T antigen (LT), without a viral origin, is sufficient to induce the hallmarks of a cellular DNA damage response (DDR), such as focal accumulation of γ-H2AX and 53BP1, via Bub1 binding. Here we expand our characterization of LT effects on the DDR. Using comet assays, we demonstrate that LT induces overt DNA damage. The Fanconi anemia pathway, associated with replication stress, becomes activated, since FancD2 accumulates in foci, and monoubiquitinated FancD2 is detected on chromatin. LT also induces a distinct set of foci of the homologous recombination repair protein Rad51 that are colocalized with Nbs1 and PML. The FancD2 and Rad51 foci require neither Bub1 nor retinoblastoma protein binding. Strikingly, wild-type LT is localized on chromatin at, or near, the Rad51/PML foci, but the LT mutant in Bub1 binding is not localized there. SV40 infection was previously shown to trigger ATM activation, which facilitates viral replication. We demonstrate that productive infection also triggers ATR-dependent Chk1 activation and that Rad51 and FancD2 colocalize with LT in viral replication centers. Using small interfering RNA (siRNA)-mediated knockdown, we demonstrate that Rad51 and, to a lesser extent, FancD2 are required for efficient viral replication in vivo, suggesting that homologous recombination is important for high-level extrachromosomal replication. Taken together, the interplay of LT with the DDR is more complex than anticipated, with individual domains of LT being connected to different subcomponents of the DDR and repair machinery.
Highly versus Normally Attractive Person in Picture Reviews

This research explored the impact of person’s physical attractiveness in the picture reviews on women’s clothing purchase intention. The results showed that the physical attractiveness of the person in the picture reviews significantly affected the purchase intention of consumers, and the highly attractive person (HAP) could promote the purchase behavior of consumers. Body image was a mediator in the relationship between person’s physical attractiveness in picture reviews and consumers’ purchase intention, that is, people’s physical attractiveness indirectly influenced consumers’ purchase intention through body image. Finally, the influence of person’s physical attractiveness on consumers’ purchase intention was moderated by perceived similarity. When the consumers perceived that the people in the pictures were similar, HAP would promote their buying behavior. However, when the consumers perceived that the people in the pictures were dissimilar, HAP would reduce their buying behavior.
Effect of body mass index on recurrences in tamoxifen and anastrozole treated women: an exploratory analysis from the ATAC trial.

PURPOSE Third-generation aromatase inhibitors have been widely used in postmenopausal women for the adjuvant treatment of hormone receptor-positive breast cancer. As aromatase inhibitors work by inhibiting the conversion of androgens to estrogens in adipose tissue, we hypothesized that anastrozole may be more effective in women with a high body mass index (BMI). PATIENTS AND METHODS The Arimidex, Tamoxifen Alone or in Combination (ATAC) study was a double-blind randomized clinical trial in which postmenopausal women with early-stage breast cancer were randomly assigned to receive oral daily anastrozole (1 mg) alone, tamoxifen (20 mg) alone, or the combination in a double-blind fashion. Analyses were based on the 100-month median follow-up for women with hormone receptor-positive breast cancers (estrogen [ER] and/or progesterone [PgR] positive). Here, we investigate the impact of BMI on recurrence and the relative benefit of anastrozole versus tamoxifen according to baseline BMI. Results Overall, women with a high BMI (BMI > 35 kg/m(2)) at baseline had more recurrences than those women with a low BMI (BMI < 23 kg/m(2); adjusted hazard ratio [HR], 1.39; 95% CI, 1.06 to 1.82; P(heterogeneity) = . 03) and significantly more distant recurrences (adjusted HR, 1.46; 95% CI, 1.07 to 1.61; P(heterogeneity) = . 01). Overall, the relative benefit of anastrozole versus tamoxifen was nonsignificantly better in thin women compared to overweight women. CONCLUSION These results confirm the poorer prognosis of obese women with early-stage breast cancer. Recurrence rates were lower for anastrozole than tamoxifen for all BMI quintiles. Our results suggest that the relative efficacy of anastrozole compared to tamoxifen is greater in thin postmenopausal women and higher doses or more complete inhibitors might be more effective in overweight women, but this requires independent confirmation.
Analysis of a meiosis-specific URS1 site: sequence requirements and involvement of replication protein A

URS1 is a transcriptional repressor site found in the promoters of a wide variety of yeast genes that are induced under stress conditions. In the context of meiotic promoters, URS1 sites act as repressor sequences during mitosis and function as activator sites during meiosis. We have investigated the sequence requirements of the URS1 site of the meiosis-specific HOP1 gene (URS1H) and have found differences compared with a URS1 site from a nonmeiotic gene. We have also observed that the sequence specificity for meiotic activation at this site differs from that for mitotic repression. Base pairs flanking the conserved core sequence enhance meiotic induction but are not required for mitotic repression of HOP1. Electrophoretic mobility shift assays of mitotic and meiotic cell extracts show a complex pattern of DNA-protein complexes, suggesting that several different protein factors bind specifically to the site. We have determined that one of the complexes of URS1H is formed by replication protein A (RPA). Although RPA binds to the double-stranded URS1H site in vitro, it has much higher affinity for single-stranded than for double-stranded URS1H, and one-hybrid assays suggest that RPA does not bind to this site at detectable levels in vivo. In addition, conditional-lethal mutations in RPA were found to have no effect on URS1H-mediated repression. These results suggest that although RPA binds to URS1H in vitro, it does not appear to have a functional role in transcriptional repression through this site in vivo.
The cannabinoid WIN 55,212‐2‐mediated protection of dentate gyrus granule cells is driven by CB1 receptors and modulated by TRPA1 and Cav2.2 channels

Cannabinoids regulate numerous physiological and pathological events like inflammation or neurodegeneration via CB1 and CB2 receptors. The mechanisms behind cannabinoid effects show a high variability and may also involve transient receptor potential channels (TRP) and N‐type voltage‐gated Ca2+ channels (Cav2.2). In the present study we investigated the neuroprotective effects of the synthetic cannabinoid WIN 55,212–2 (WIN) on dentate gyrus (DG) granule cells and elucidated the involvement of TRP and Cav2.2 that are shown to participate in inflammatory processes. Organotypic hippocampal slice cultures were excitotoxically lesioned using NMDA and subsequently incubated with different WIN concentrations (0.001–10 μM). WIN showed neuroprotective properties in an inverse concentration‐dependent manner, most effectively at 0.01 μM. The CB1 receptor antagonist AM251 blocked neuroprotection mediated by WIN whereas the CB2 receptor antagonist AM630 showed no effects. Application of the TRPA1 blocker HC‐030031 enhanced the neuroprotective efficacy of high (10 μM) WIN concentrations and the number of degenerating neurons became equal to that seen after application of the most effective WIN dose (0.01 μM). In contrast, the application of TRPA1 agonist icilin or allyl isothiocyanate (AITC) led to a stronger neurodegeneration. The use of TRPV1 blocker 6‐iodo‐nordihydrocapsaicin did not affect WIN‐mediated neuroprotection. The selective Cav2.2 blocker ω‐conotoxin (GVIA) completely blocked neuroprotection shown by 10 μM WIN. GVIA and HC‐030031 exerted no effects at WIN concentrations lower than 10 μM. Our data show that WIN protects dentate gyrus granule cells in a concentration dependent manner by acting upon CB1 receptors. At high (10 μM) concentrations WIN additionally activates TRPA1 and Cav2.2 within the hippocampal formation that both interfere with CB1 receptor‐mediated neuroprotection. This leads to the conclusion that physiological and pharmacological effects of cannabinoids strongly depend on their concentration and the neuroprotective efficacy of cannabinoids may be determined by interaction of activated CB1 receptor, TRPA1, and Cav2.2. © 2010 Wiley‐Liss, Inc.