julilili42/papers huggingface dataset:
Amplified pathogenic actions of angiotensin II in cysteine‐rich LIM‐only protein 4–negative mouse hearts
2017-01-30

LIM domain proteins have been identified as essential modulators of cardiac biology and pathology; however, it is unclear which role the cysteine‐rich LIM‐only protein (CRP)4 plays in these processes. In studying CRP4 mutant mice, we found that their hearts developed normally, but lack of CRP4 exaggerated multiple parameters of the cardiac stress response to the neurohormone angiotensin II (Ang II). Aiming to dissect the molecular details, we found a link between CRP4 and the cardioprotective cGMP pathway, as well as a multiprotein complex comprising well‐known hypertrophy‐associated factors. S ignificant enrichment of the cysteine‐rich intestinal protein (CRIP)1 in murine hearts lacking CRP4, as well as severe cardiac defects and premature death of CRIP1 and CRP4 morphant zebrafish embryos, further support the notion that depleting CRP4 is incompatible with a proper cardiac development and function. Together, amplified Ang II signaling identified CRP4 as a novel antiremodeling factor regulated, at least to some extent, by cardiac cGMP. —Straubinger, J., Boldt, K., Kuret, A., Deng, L., Krattenmacher, D., Bork, N., Desch, M., Feil, R., Feil, S., Nemer, M., Ueffing, M., Ruth, P., Just, S., Lukowski, R. Amplified pathogenic actions of angio‐tensin II in cysteine‐rich LIM‐only protein 4 negative mouse hearts. FASEB J . 31, 1620–1638 (2017) www.fasebj.org
Divergent morphologies of adhesive predatory mouthparts of Stenus species (Coleoptera: Staphylinidae) explain differences in adhesive performance and resulting prey-capture success
2017-01-30

Members of the genus Stenus (Coleoptera, Staphylinidae) possess a unique adhesive labial prey-capture apparatus as an adaptation to their predatory behaviour. In order to examine the relationships between the morphology of the prey-capture apparatus, its adhesive performance and the prey-capture success, we combined force measurements, morphological and behavioural investigations of representatives of 14 Central European species of this genus. The direct relationship between these traits was studied by using phylogenetic generalized least squares and a molecular phylogeny generated from mitochondrial cytochrome c oxidase I partial sequences. Force measurements revealed strong interspecific differences in the adhesive forces generated during the predatory attack; these differences entail significant differences in the prey-capture success. The interspecific differences in adhesive performance were functionally correlated with the pad morphology and divergences in the compressive forces generated during the predatory strike. Allometric analyses revealed that the pad area scaled with positive allometry with respect to body size, whereas the adhesive forces scaled with negative allometry with respect to body size, that is, the pads' efficiency decreased with body size. Our experimental approach demonstrates a direct functional relationship between the morphology of the prey-capture device of Stenus beetles and its performance in a natural behavioural context.
Influence of Work Pace on Upper Extremity Kinematics and Muscle Activity in a Short-Cycle Repetitive Pick-and-Place Task
2017-01-30

The present study did not find any consistent work pace effect on upper extremity kinematics and muscle activity, in spite of a comprehensive empirical basis compared to previous literature. While our results suggest that work pace may not be of critical concern in an occupational health context, we encourage further studies verifying or disproving this notion.
Brain–Computer Interface–Based Communication in the Completely Locked-In State
2017-01-31

Despite partial success, communication has remained impossible for persons suffering from complete motor paralysis but intact cognitive and emotional processing, a state called complete locked-in state (CLIS). Based on a motor learning theoretical context and on the failure of neuroelectric brain-computer interface (BCI) communication attempts in CLIS, we here report BCI communication using functional near-infrared spectroscopy (fNIRS) and an implicit attentional processing procedure. Four patients suffering from advanced amyotrophic lateral sclerosis (ALS)-two of them in permanent CLIS and two entering the CLIS without reliable means of communication-learned to answer personal questions with known answers and open questions all requiring a "yes" or "no" thought using frontocentral oxygenation changes measured with fNIRS. Three patients completed more than 46 sessions spread over several weeks, and one patient (patient W) completed 20 sessions. Online fNIRS classification of personal questions with known answers and open questions using linear support vector machine (SVM) resulted in an above-chance-level correct response rate over 70%. Electroencephalographic oscillations and electrooculographic signals did not exceed the chance-level threshold for correct communication despite occasional differences between the physiological signals representing a "yes" or "no" response. However, electroencephalogram (EEG) changes in the theta-frequency band correlated with inferior communication performance, probably because of decreased vigilance and attention. If replicated with ALS patients in CLIS, these positive results could indicate the first step towards abolition of complete locked-in states, at least for ALS.
Evolutionary responses to land use in eight common grassland plants
2017-01-31

Summary Land‐use change is an important component of global environmental change and a major driver of current declines in biodiversity. Although there is increasing evidence that species can evolve rapidly in response to anthropogenic environmental change, comprehensive studies of the evolutionary consequences of land use are still fairly scarce, in particular such that consider multiple species, study many populations, or that discriminate between different aspects of land use. Here, we studied genetic change of key phenotypic traits in response to land use in eight common grassland species across 137 grassland sites covering a broad range of land‐use types (mowing and/or grazing, with or without fertilization) and intensities in three regions of Germany. A common garden study revealed significant genetic differentiation in response to land‐use intensification within all of the investigated species. Among the studied land‐use processes, mowing appeared to have the strongest effect on the differentiation of plant phenotypes, with flowering phenology as the most responsive trait. However, there was substantial variation among species in the magnitude, sometimes also the direction of the observed population differentiation. Synthesis . Our study demonstrates that evolutionary responses of grassland plants to land‐use change are a common phenomenon and widespread across a broad range of different species. These evolutionary changes are likely to impact biotic interactions, as well as the structure and functioning of communities and ecosystems.
Progress Towards a Public Chemogenomic Set for Protein Kinases and a Call for Contributions
2017-01-31

Abstract Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.
A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and “pan-leukemia” antigens
2017-01-31

Hematological malignancies (HM) are highly amenable targets for immunotherapeutic intervention and may be effectively treated by antigen-specific T-cell based treatment. Recent studies demonstrate that physiologically occurring anti-cancer T-cell responses in certain HM entities target broadly presented non-mutated epitopes. HLA ligands are thus implied as prime targets for broadly applicable and antigen-specific off-the-shelf compounds. With the aim of assessing the presence of common targets shared among different HM which may enable addressing a larger patient collective we conducted a meta-analysis of 83 mass spectrometry-based HLA peptidome datasets (comprising 40,361 unique peptide identifications) across four major HM (19 AML, 16 CML, 35 CLL, and 13 MM/MCL samples) and investigated similarities and differences within the HLA presented antigenic landscape. We found the cancer HLA peptidome datasets to cluster specifically along entity and lineage lines, suggesting that the immunopeptidome directly reflects the differences in the underlying (tumor-)biology. In line with these findings, we only detected a small set of entity-spanning antigens, which were predominantly characterized by low presentation frequencies within the different patient cohorts. These findings suggest that design of T-cell immunotherapies for the treatment of HM should ideally be conducted in an entity-specific fashion.
Haemorrhagic Transformation after Ischaemic Stroke in Patients Taking Non-vitamin K Antagonist Oral Anticoagulants
2017-01-31

The frequency and severity of HT after stroke on NOAC appears similar to previous reports for vitamin K antagonists and no anticoagulation. Whether asymptomatic HT should delay resumption of preventive anticoagulation requires further investigation.
Progressive Perforation of the Nasal Septum Due to Leishmania major: A Case of Mucosal Leishmaniasis in a Traveler
2017-01-31

This report describes a case of mucosal leishmaniasis caused by Leishmania major with destructive perforation of the nasal septum illustrating the diagnostic challenges of a rare clinical presentation of L. major infection in a traveler. The atypical presentation may have been associated with the use of cortisone as a potential trigger for the progressive destruction of the nasal septum.
Recent advances and future directions in mantle cell lymphoma research: report of the 2016 mantle cell lymphoma consortium workshop
2017-01-31

Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma typically associated with the t(11;14) chromosomal translocation, resulting in overexpression of cyclin D1. Although MCL is associated with clinical heterogeneity, outcomes are generally poor and no standard treatment has been established. However, the recent approval of ibrutinib provides a new therapeutic option. Moreover, recent clinical trials have provided new perspectives on the relative efficacy and safety of various approaches for both transplant-eligible and transplant-ineligible patients. Multiple novel strategies are being evaluated in the treatment of MCL, including both targeted agents and cellular immunotherapies. At the Lymphoma Research Foundation's 12th MCL Workshop, researchers gathered to discuss research findings, clinical trial results, and future directions related to MCL, its biology, and its treatment. This manuscript, which includes a summary of each presentation, aims to review recent findings in MCL research and highlight potential areas for future study.
Current and prospective sights in mechanism of deoxynivalenol‐induced emesis for future scientific study and clinical treatment
2017-01-31

Abstract Deoxynivalenol (DON), one of trichothecene mycotoxins produced by the fungus Fusarium , is commonly detected in cereal foods and in secondary food production across the world. Lower concentrations of DON induce a dose‐related feed refusal (anorexia), whereas it acts as a potent emetic agent at higher levels. DON‐induced emesis in humans and livestock can be observed and recorded in both undeveloped and developed regions such as Lixian, Guide and Huangzhong in China and Illinois in the USA. Some studies with different animal models (pigs and minks) suggested that DON could change expressions of 5‐hydroxytryptamine, peptide YY, neuropeptide Y2 receptor and nucleobindin‐2/nesfatin‐1 in plasma and different areas of the brain. Some selective antagonist of 5‐hydroxytryptamine 3 receptors can inhibit DON‐induced emetic response. Otherwise, the Ca 2+ homeostasis and MAPK pathway could be potential directions in future studies. Dolasetron, dantrolene and JNJ‐31020028 can be used in clinical treatment but they have potential toxic effects. (−)Epicatechin, ginger phytochemicals and isoflavone can be tested in in vitro and in vivo for their usage as food additives for reducing the emesis. The present review summarizes and discusses some information from previous and recent prominent publications with the aim to provide some comprehensive and helpful data for understanding the mechanism of DON‐induced emesis. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Carbon Sources in Fruit Carbonate of Buglossoides arvensis and Consequences for 14C Dating
2017-01-31

Abstract Fruit carbonate of Buglossoides arvensis (syn. Lithospermum arvense ) is a valuable dating and paleoenvironmental proxy for late Quaternary deposits and cultural layers because CaCO 3 in fruit is assumed to be accumulated from photosynthetic carbon (C). However, considering the uptake of HCO 3 – by roots from soil solution, the estimated age could be too old depending on the source of HCO 3 – allocated in fruit carbonate. Until now, no studies have assessed the contributions of photosynthetic and soil C to the fruit carbonate. To evaluate this, the allocation of photo-assimilated carbon and root uptake of HCO 3 – was examined by radiocarbon ( 14 C) labeling and tracing. B. arvensis was grown in carbonate-free and carbonate-containing soils (sand and loess, respectively), where 14 C was provided as (1) 14 CO 2 in the atmosphere (5 times shoot pulse labeling), or (2) Na 2 14 CO 3 in soil solution (root-labeling; 5 times by injecting labeled solution into the soil) during one month of fruit development. Distinctly different patterns of 14 C distribution in plant organs after root- and shoot labeling showed the ability of B. arvensis to take up HCO 3 – from soil solution. The highest 14 C activity from root labeling was recovered in roots, followed by shoots, fruit organics, and fruit carbonate. In contrast, 14 C activity after shoot labeling was the highest in shoots, followed by fruit organics, roots and fruit carbonate. Total photo-assimilated C incorporated via shoot labeling in loess-grown plants was 1.51 mg lower than in sand, reflecting the presence of dissolved carbonate (i.e. CaCO 3 ) in loess. Loess carbonate dissolution and root-respired CO 2 in soil solution are both sources of HCO 3 – for root uptake. Considering this dilution effect by carbonates, the total incorporated HCO 3 – comprised 0.15% of C in fruit carbonate after 10 hr of shoot labeling. However, if the incorporated HCO 3 – during 10 hr of shoot labeling is extrapolated for the whole month of fruit development (i.e. 420-hr photoperiod), fruit carbonate in loess-grown plants incorporated approximately 6.3% more HCO 3 – than in sand. Therefore, fruit carbonates from plants grown on calcareous soils may yield overestimated 14 C ages around 500 yr because of a few percentage uptake of HCO 3 – by roots. However, the age overestimation because of HCO 3 – uptake becomes insignificant in fruits older than approximately 11,000 yr due to increasing uncertainties in age determination.
Global integration and world migration
2017-01-31

This paper explores the following chain of conjectures: rising use of the internet, the widespread access to global information, and intensified communication between regions and countries brought about, for example, by intensified trade links bring about expansion of people’s social space and their set of comparators; this expansion increases people’s stress and strengthens their inclination to resort to migration as a means of reducing this heightened stress. Other things held constant, the expansion of people’s social space intensifies their inclination to move across geographical space.
Learning Historical Thinking With Oral History Interviews: A Cluster Randomized Controlled Intervention Study of Oral History Interviews in History Lessons
2017-02-01

The present study examined the effectiveness of the oral history approach with respect to students’ historical competence. A total of 35 ninth-grade classes ( N = 900) in Germany were randomly assigned to one of four conditions—live, video, text, or a (nontreated) control group—in a pretest, posttest, and follow-up design. Comparing the three intervention groups with the control group, the intervention groups scored better on four of the five achievement tests. Comparing the live group with the video and text groups, students in the live condition were more convinced of their learning progress at both measurement points. However, they scored lower than the video/text group on two achievement measures and higher on one at the posttest.
Extraction of Ultrashort DNA Molecules from Herbarium Specimens
2017-02-01

DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.
Examining the Relationship Between Children’s ADHD Symptomatology and Inadequate Parenting: The Role of Household Chaos
2017-02-01

Objective: This study examines the interrelations of parenting practices, emotional climate, and household chaos in families with children with and without ADHD. In particular, indirect pathways from children’s ADHD symptomatology to inadequate parenting and negative emotional climate via household chaos were investigated. Method: Parenting, emotional climate, and household chaos were assessed using questionnaires and a speech sample of parents of 31 children with and 53 without ADHD, aged 7 to 13 years. Results: Group differences were found for certain parenting dimensions, the parent–child relationship, critical comments, and household chaos. While we found significant indirect effects between children’s ADHD and certain parenting dimensions through household chaos, no effects were found for any aspect of emotional climate. Conclusion: Children’s ADHD symptoms translate into inadequate parenting through household chaos, which underlines the need for interventions to improve household organization skills in parents of children with ADHD.
A randomized, double-blind, multicenter phase III study evaluating paclitaxel with and without RAD001 in patients with gastric cancer who have progressed after therapy with a fluoropyrimidine/platinum-containing regimen (RADPAC).
2017-02-01

4 Background: There is a need for effective treatments in the second- or further line setting in advanced gastric cancer, especially for new agents. In the current trial we evaluated paclitaxel with RAD001 (everolimus) in patients with gastric carcinoma who have progressed after therapy with a fluoropyrimidine/platinum-containing regimen. Methods: This is a randomized, double-blind, multi-center phase III study. Patients with gastric carcinoma or adenocarcinoma of the esophagogastric junction which has progressed after treatment with a fluoropyrimidine/platinum-containing regimen were randomly assigned to receive Paclitaxel (80 mg/m2) on day 1, 8 and 15 plus placebo (arm A) or RAD001 (10mg daily, arm B) d1-d28, repeated every 28 days as 2 nd , 3 rd or 4 th line therapy. Primary end point was overall survival (OS), secondary endpoints were best overall response, disease control rate, progression free survival (PFS) and toxicity. Results: 300 patients (median age: 62 years; median lines prior therapy: 2) were randomly assigned (Arm A, 150, Arm B, 150). Response rate (complete and partial response) was 8.0% (95%CI: 4.2%-13.6%) in the paclitaxel/RAD001 arm and 7.3% (95% CI: 3.7%-12.7%) in the paclitaxel/placebo arm (p = 0.4).There was no significant difference in median PFS (placebo, 2.07 vs. RAD001, 2.2 months, HR 0.88, p = 0.3) and median OS (placebo, 5.1 vs. RAD001, 6.1 months, HR 0.92, p = 0.48). Combination of paclitaxel and RAD001 was tolerable, but the placebo arm was associated with significantly less (any grade) mucositis (15.8% vs. 37.2%), fever (10.3% vs 20.7%), leukopenia (11.6% vs. 21.4%), neutropenia (13.0% vs. 27.6%) and thrombocytopenia (2.1% vs 14.5%). Conclusions: The addition of RAD001 to paclitaxel/RAD001 did not significantly improve outcomes in pretreated metastatic gastric or esophagogastric junction adenocarcinoma. Additional biomarker studies are planned to look for subgroups that may have a benefit. Clinical trial information: NCT01248403.
Intersection-Link Representations of Graphs
2017-02-01

We consider drawings of graphs that contain dense subgraphs. We introduce intersection-link representations for such graphs, in which each vertex is represented by a geometric object and each edge is represented by the intersection between and , if it belongs to a dense subgraph, or by a curve connecting the boundaries of and , otherwise. We study a notion of planarity, called , for intersection-link representations of graphs in which the dense subgraphs are cliques.
Accurate Radiocarbon Dating of Archaeological Ash Using Pyrogenic Aragonite
2017-02-01

Abstract Obtaining accurate age determinations from minerals in archaeological ash is a major unsolved issue in radiocarbon ( 14 C) dating. This is because the original 14 C content of calcite, the main component of ash, is altered by isotopic exchange. Pyrogenic aragonite, another mineral phase recently discovered in ash, might preserve its 14 C signature through time. Using a new method based on density separation and step combustion, we were able to isolate and date aragonitic ash from an archaeological destruction horizon of known age. Here we show that the 14 C age of aragonite matches the age of the destruction horizon. Our results demonstrate that pyrogenic aragonite is a short-lived material suitable for 14 C dating and directly related to human activities involving the use of fire, thus bearing major implications for the establishment of absolute chronologies for the past 50,000 yr.