bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Pilot Study of Cognitive Impairment in Longstanding Electroconvulsive Therapy–treated Schizophrenia Patients Versus Controls
Authors: Danenberg Renana , Ruimi Liad , Shelef Assaf , Paleacu Kertesz Diana 
Published: July 2020

Background
Electroconvulsive therapy (ECT), though reliable and effective, is controversial due to its media portrayal as a treatment with severe side effects. Electroconvulsive therapy is mainly given to patients suffering from affective disorders and treatment-resistant schizophrenia. Although past research assessed the amount and duration of memory loss due to ECT, little is known about its influence on cognition for patients suffering from schizophrenia, whose cognitive decline is an inherent part of their illness. We aimed to test whether maintenance ECT causes cognitive decline among elderly schizophrenia patients.

Methods
Twenty elderly (age >65 years) patients suffering from schizophrenia and schizoaffective disorder who received maintenance ECT were matched with 20 controls suffering from the same illnesses that have never been treated with ECT. The match was based on age, sex, and illness duration. The participants were evaluated using the Montreal Cognitive Assessment for cognitive decline and a Positive and Negative Syndrome Scale (PANSS) for illness severity.

Results
A lower score in the abstraction subscale was found in the maintenance ECT population (P = 0.002), without significant differences in the total Montreal Cognitive Assessment and the delayed-recall subscale scores. In the treatment group, a correlation was found between an impairment in naming and positive symptoms in the PANSS score (r = −0.45) and between abstraction impairment and negative symptoms (r = −0.56) and total PANSS score (r = −0.497).

Conclusions
Maintenance ECT does not worsen existing global cognitive deficits or delayed recall in elderly schizophrenia patients. The abstraction impairment was possibly due to the higher disease burden of the patients referred to ECT.
Nitrogen deposition is negatively related to species richness and abundance of threatened species in Swiss butterflies
Authors: Roth Tobias , Kohli Lukas , Rihm Beat , Meier Reto , Amrhein Valentin 
Published: July 2020

AbstractNitrogen (N) deposition caused by agriculture and combustion of fossil fuels is a major threat to plant diversity, but the effects on higher trophic levels are less clear. In this study we investigated how N deposition may affect species richness and abundance (number of individuals per species) in butterflies. We started with reviewing the literature and found that vegetation parameters might be as important as climate and habitat variables in explaining variation in butterfly species richness. It thus seems likely that increased N deposition indirectly affects butterfly communities via its influence on plant communities. We then analysed data from the Swiss biodiversity monitoring program surveying species diversity of vascular plants and butterflies in 383 study sites of 1 km2 that are regularly distributed over Switzerland, covering a modelled N deposition gradient from 2 to 44 kg N ha −1 yr−1. Using traditional linear models and structural equation models, we found that high N deposition was consistently linked to low butterfly diversity, suggesting a net loss of butterfly diversity through increased N deposition. At low elevations, N deposition may contribute to a reduction in butterfly species richness via microclimatic cooling due to increased plant biomass. At higher elevations, negative effects of N deposition on butterfly species richness may also be mediated by reduced plant species richness. In most butterfly species, abundance was negatively related to N deposition, but the strongest negative effects were found for species of conservation concern. We conclude that in addition to factors such as intensified agriculture, habitat fragmentation and climate change, N deposition is likely to play a key role in negatively affecting butterfly diversity and abundance.Article Impact StatementNitrogen deposition negatively affects butterfly species richness and butterfly abundance, particularly in species of conservation concern.Data accessibility and reproducibility of resultsData and R-scripts to reproduce the results of this manuscript including figures and tables are provided at https://github.com/TobiasRoth/NDep_butterflies. Raw data for analyses are provided in the folder “data”, and the folder “R” contains the R-Script that was used to export the data from the BDM database and to produce the figures and tables of the manuscript.
CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase
Authors: Lu Yang Young , Bai Jiaxing , Wang Yiwen , Wang Ying , Sun Fengzhu 
Published: July 2020

AbstractMotivationRapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based onk-mer frequencies offers a computationally efficient solution, yet in practice, thek-mer frequency vectors for largekof practical interest lead to excessive memory and storage consumption.ResultsWe report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing (HTS) data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102– 104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.AvailabilityCRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available athttps://github.com/jiaxingbai/CRAFT.Contactwangying@xmu.edu.cn;fsun@usc.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Authors: McClenaghan Beverly , Fahner Nicole , Cote David , Chawarski Julek , McCarthy Avery , Rajabi Hoda , Singer Greg , Hajibabaei Mehrdad 
Published: July 2020

AbstractThe deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here, we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea water samples. We found that deep sea water samples (> 1400 m depth) had significantly lower DNA concentrations than surface or mid-depth samples necessitating a refined protocol with a larger sampling volume. We recovered significantly more DNA in large volume water samples (1.5 L) filtered at sea compared to small volume samples (250 mL) held for lab filtration. Furthermore, the number of unique sequences (exact sequence variants; ESVs) recovered per sample was higher in large volume samples. Since the number of ESVs recovered from large volume samples was less variable and consistently high, we recommend the larger volumes when sampling water from the deep ocean. We also identified three primer sets which detected the most fish taxa but recommend using multiple markers due the variability in detection probabilities and taxonomic resolution among fishes for each primer set. Overall, fish diversity results obtained from metabarcoding were comparable to conventional survey methods. While eDNA sampling and processing need be optimized for this unique environment, the results of this study demonstrate that eDNA metabarcoding can be employed to facilitate biodiversity surveys in the deep ocean, require less dedicated survey effort per unit identification and are capable of simultaneously providing valuable information on other taxonomic groups.
Loss of Circadian Protection in Adults Exposed to Neonatal Hyperoxia
Authors: Issah Yasmine , Naik Amruta , Tang Soon Y , Forrest Kaitlyn , Brooke Thomas G , Lahens Nicholas , Theken Katherine N. , Sehgal Amita , Worthen George S. , FitzGerald Garret A. , Sengupta Shaon 
Published: July 2020

AbstractAdverse early life exposures having a lasting negative impact on health. For examples, neonatal hyperoxia which is a risk factor for chronic lung disease of prematurity or bronchopulmonary dysplasia (BPD) confers susceptibility to respiratory infections like Influenza A (IAV) later in life. Given our previous findings that the circadian clock exerts a protective effect on injury from IAV, we asked if the long-term impact of neonatal hyperoxia includes disruption of circadian rhythms. We show here that neonatal hyperoxia abolishes the circadian clock mediated time of day protection from IAV, not through the regulation of viral burden, but through host tolerance pathways. We further discovered that that this dysregulation is mediated through the intrinsic clock in the lung, rather than through central or immune system clocks. Loss of circadian protein,Bmal1, in AT2 cells of the lung recapitulates the increased mortality, loss of temporal gating and other key features of hyperoxia-exposed animals. Taken together, our data suggest a novel role for the circadian clock in AT2 clock in mediating long-term effects of early life exposures to the lungs.Brief SummaryNeonatal hyperoxia abrogates the circadian protection from Influenza infection in recovered adults.
Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location
Authors: Cocking Jill Hager , Turley Sgt. Ryan , Fofanov Viacheslav Y. , Samuels-Crow Kimberly , Hungate Bruce , Mau Rebecca L. , Keim Paul S. , Caporaso J. Gregory , Hepp Crystal 
Published: July 2020

ABSTRACTOver the past two decades, advances in molecular biology have greatly expanded our understanding of microbiomes – the diverse assemblages of microorganisms that inhabit the human body as well as the world around us, and applications in microbiome science have become an active area of research. Differences in the diversity (i.e., richness) and composition of microbiomes has been found to be informative in varied areas of science, including human health, agronomy, and forensic science. Soil harbors microbiomes that vary based on many factors, including the geology of the soil (e.g., sand, silt, or clay), climate, and use of the soil. As a result, the microbiological composition of any two soil samples will never be exactly alike. This inherent variation between microbiomes of different locations has proven to be specific enough to be potentially useful in forensic investigations to associate a person or piece of evidence to a source site.In this study, a soil microbiome was extracted from the sock of a criminal suspect and compared to the microbiome of soil samples taken from locations traveled to by the suspect. The locations analyzed varied in their soil microbiome composition, and the microbiome profiled from the sock was found to be most similar to the location where the suspect was thought to have left the body of a murder victim. These results provide a case study illustrating that information contained in a soil microbiome may be applied to link evidence to the location where a crime took place, potentially serving as an investigative tool in law enforcement.
Abandonment and restoration of Mediterranean meadows: long-term effects on a butterfly-plant network
Authors: Colom Pau , Traveset Anna , Stefanescu Constantí 
Published: July 2020

AbstractBoth the intensification and abandonment of traditional agricultural practices are known to be major threats to biodiversity worldwide, above all in industrialized countries. Although land abandonment in particular has a negative effect on the diversity of both plant and insect communities, few studies have ever analysed these two groups together and none has yet examined the effect on plant-insect interactions using a network approach. In view of the notable decline of pollinator insects reported in past decades, it is essential to understand how the structure of a plant-pollinator network changes during the ecological succession that occurs as traditionally managed habitats are abandoned, and to what extent this network is re-established when habitats are restored. We monitored a butterfly-plant network for 22 years in habitats where land abandonment and restoration have taken place and were able to compare restoration by grazing with restoration combining mowing and grazing. Abandonment leads to significant reductions in the cover of typical grasslands plants and, in turn, rapidly provokes changes in butterfly assemblages and plant interactions. Specifically, it caused a replacement of multivoltine by monovoltine species, increasing network specialization due to the great specificity in the interactions that monovoltine species established with plants. Changes in butterfly communities were also recorded in a nearby unaltered habitat due to the metapopulation structure of some species. A highly dynamic source-sink system was established between managed and unmanaged habitat patches, which ultimately allowed the metapopulations to persist. Restoration combining mowing and grazing promoted a quick return to the pre-abandonment situation in the butterfly community, and also increased generality and nestedness, two network descriptors that are known to enhance community stability.
An orthogonal differentiation platform for genomically programming stem cells, organoids, and bioprinted tissues
Authors: Skylar-Scott Mark A. , Huang Jeremy Y. , Lu Aric , Ng Alex H.M. , Duenki Tomoya , Nam Lucy L. , Damaraju Sarita , Church George M. , Lewis Jennifer A. 
Published: July 2020

AbstractSimultaneous differentiation of human induced pluripotent stem cells (hiPSCs) into divergent cell types offers a pathway to achieving tailorable cellular complexity, patterned architecture, and function in engineered human organoids and tissues. Recent transcription factor (TF) overexpression protocols typically produce only one cell type of interest rather than the multitude of cell types and structural organization found in native human tissues. Here, we report an orthogonal differentiation platform for genomically programming stem cells, organoids and bioprinted tissues with controlled composition and organization. To demonstrate this platform, we orthogonally differentiated endothelial cells and neurons from hiPSCs in a one-pot system containing neural stem cell-specifying media. By aggregating inducible-TF and wildtype hiPSCs into pooled and multicore-shell embryoid bodies, we produced vascularized and patterned cortical organoids within days. Using multimaterial 3D bioprinting, we patterned 3D neural tissues from densely cellular, matrix-free stem cell inks that were orthogonally differentiated on demand into distinct layered regions composed of neural stem cells, endothelium, and neurons, respectively. Given the high proliferative capacity and patient-specificity of hiPSCs, our platform provides a facile route for programming cells and multicellular tissues for drug screening and therapeutic applications.
Does the Preferred Walk-Run Transition Speed on Inclines Minimize Energetic Cost, Heart Rate or Neither?
Authors: Brill Jackson W. , Kram Rodger 
Published: July 2020

ABSTRACTHumans prefer to walk at slow speeds and to run at fast speeds. In between, there is a speed at which people choose to transition between gaits, the Preferred Transition Speed (PTS). At slow speeds, it is energetically cheaper to walk and at faster speeds, it is cheaper to run. Thus, there is an intermediate speed, the Energetically Optimal Transition Speed (EOTS). Our goals were to determine: 1) how PTS and EOTS compare across a wide range of inclines and 2) if the EOTS can be predicted by the heart rate optimal transition speed (HROTS). Ten healthy, high-caliber, male trail/mountain runners participated. On day 1, subjects completed 0° and 15° trials and on day 2, 5° and 10°. We calculated PTS as the average of the walk-to-run transition speed (WRTS) and the run-to-walk transition speed (RWTS) determined with an incremental protocol. We calculated EOTS and HROTS from energetic cost and heart rate data for walking and running near the expected EOTS for each incline. The intersection of the walking and running linear regression equations defined EOTS and HROTS. We found that PTS, EOTS, and HROTS all were slower on steeper inclines. PTS was slower than EOTS at 0°, 5°, and 10°, but the two converged at 15°. PTS and EOTS were only moderately correlated. Although EOTS correlated with HROTS, EOTS was not predicted accurately by heart rate on an individual basis.
Prostaglandin E2 promotes intestinal inflammation via inhibiting microbiota-dependent regulatory T cells
Authors: Crittenden Siobhan , Goepp Marie , Pollock Jolinda , Robb Calum T. , Smyth Danielle J. , Zhou You , Andrews Robert , Tyrrell Victoria , Adima Alexander , O’Connor Richard A. , Davies Luke , Li Xue-Feng , Yao Hatti X. , Ho Gwo-Tzer , Zheng Xiaozhong , Mair Amil , Vermeren Sonja , Qian Bin-Zhi , Mole Damian J. , Schwarze Jürgen K.J. , Breyer Richard M. , Arends Mark J. , O’Donnell Valerie B. , Iredale John P. , Anderton Stephen M. , Narumiya Shuh , Maizels Rick M. , Rossi Adriano G. , Howie Sarah E. , Yao Chengcan 
Published: July 2020

AbstractThe gut microbiota fundamentally regulates intestinal homeostasis and disease partially through mechanisms that involve modulation of regulatory T cells (Tregs), yet how the microbiota-Treg crosstalk is physiologically controlled is incompletely defined. Here, we report that prostaglandin E2 (PGE2), a well-known mediator of inflammation, inhibits mucosal Tregs in a manner depending on the gut microbiota. PGE2 through its receptor EP4 diminishes Treg-favorable commensal microbiota. Transfer of the gut microbiota that was modified by PGE2-EP4 signaling modulates mucosal Treg responses and exacerbates intestinal inflammation. Mechanistically, PGE2-modified microbiota regulates intestinal mononuclear phagocytes and type I interferon signaling. Depletion of mononuclear phagocytes or deficiency of type I interferon receptor contracts PGE2-dependent Treg inhibition. Taken together, our findings provide emergent evidence that PGE2-mediated disruption of microbiota-Treg communication fosters intestinal inflammation.
Cancer-associated fibroblasts in pancreatic ductal adenocarcinoma determine response to SLC7A11 inhibition
Authors: Sharbeen George , McCarroll Joshua A. , Akerman Anouschka , Kopecky Chantal , Youkhana Janet , Holst Jeff , Boyer Cyrille , Erkan Mert , Goldstein David , Timpson Paul , Cox Thomas R. , Pereira Brooke A. , Chitty Jessica L. , Fey Sigrid , Najumudeen Arafath K. , Campbell Andrew D. , Sansom Owen J. , Ignacio Rosa Mistica C. , Naim Stephanie , Liu Jie , Russia Nelson , Lee Julia , Chou Angela , Johns Amber , Gill Anthony , Gonzales-Aloy Estrella , Kokkinos John , Gebski Val , Turner Nigel , Apte Minoti , Davis Thomas P. , Morton Jennifer P. , Haghighi Koroush ,   Australian Pancreatic Cancer Genome Initiative, Phillips Phoebe A. 
Published: July 2020

ABSTRACTCancer-Associated Fibroblasts (CAFs) are major contributors to pancreatic ductal adenocarcinoma (PDAC) progression, through pro-tumour cross-talk and the generation of fibrosis (physical barrier to drugs). CAF inhibition is thus an ideal component of any therapeutic approach for PDAC. SLC7A11 is a cystine transporter that has been identified as a potential therapeutic target in PDAC cells. However, no prior study has evaluated the role of SLC7A11 in PDAC tumour stroma and its prognostic significance. Herein we show that high expression of SLC7A11 in PDAC tumour stroma (but not tumour cells) is independently prognostic of poorer overall survival. We demonstrate using orthogonal approaches that PDAC-derived CAFs are highly dependent on SLC7A11 for cystine uptake and glutathione synthesis, and that SLC7A11 inhibition significantly decreases their proliferation, reduces their resistance to oxidative stress and inhibits their ability to remodel collagen and support PDAC cell growth. Importantly, our paradigm-shifting work demonstrates the need to inhibit SLC7A11 in the PDAC stroma, as genetic ablation of SLC7A11 in PDAC cells alone is not enough to reduce tumour growth. Finally, our work validates that a nano-based gene-silencing drug against SLC7A11, developed by our group, reduces PDAC tumour growth, CAF activation and fibrosis in a mouse model of PDAC.
The role of musical priming in brand recall
Authors: Levrini Gabriel , Schaeffer Cristian Luis , Nique Walter 
Published: July 2020

PurposeThe purpose of this paper is twofold: first, to analyze whether musical priming induces greater recall of brands and, second, to study the emotional priming effects of music, in comparison with non-emotional music, including gender comparison.Design/methodology/approachThrough the utilization of neuromarketing tools and protocols (quantitative and qualitative), the study explores facial eltromyography (EMG) capabilities and skin conductance responses (SCR) measuring consumers’ emotional responses.FindingsThe findings show that at least, 40 percent of the total sample recognized a musical priming effect. The study measures the emotional response to musical priming as positive. Emotional video recognition was much higher in females. Both the self-report and physiological measures support the notion that emotional background music can elicit emotional responses in consumers.Research limitations/implicationsThe research measured emotional response to musical priming without testing how these responses influence consumers’ attention and overall behavior.Practical implicationsThe five senses, especially hearing, play an important role in the purchasing decision process and in the individual customer experience. People become aware of the products and brands that surround them and make their choice. In terms of digital trading activities and online sales, increasing physiological understanding of musical priming reactions may mean that, for companies, selling low-end online goods may be economically worthwhile to cooperate with platforms such as Spotify or iTunes to select individual users.Social implicationsMore research is needed in priming process techniques in order to better understand how primes activate knowledge in the consumer’s mind. Understanding this process will inform marketers how close a prime needs to be to a target to have an effective influence, as well as when marketers should be concerned about negative priming effects.Originality/valueAt the best of our knowledge, it is the first time that music priming is analyzed in terms of self-report and physiological measures From the measurement’s perspective, the results reaffirm that physiological and self-report measures capture different levels of information. While SCR and EMG capture real-time subconscious responses, MAN scale self-report data provide information regarding how cognitive effort, in terms of intensity and valence, affects brand recall.