bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age-related transcriptome changes in Sox2+ supporting cells in the mouse cochlea
Authors: Cheng Cheng , Wang Yunfeng , Guo Luo , Lu Xiaoling , Zhu Weijie , Muhammad Waqas , Zhang Liyan , Lu Ling , Gao Junyan , Tang Mingliang , Chen Fangyi , Gao Xia , Li Huawei , Chai Renjie 
Published: December 2019

AbstractBackgroundInner ear supporting cells (SCs) in the neonatal mouse cochlea are a potential source for hair cell (HC) regeneration, but several studies have shown that the regeneration ability of SCs decreases dramatically as mice age and that lost HCs cannot be regenerated in adult mice. To better understand how SCs might be better used to regenerate HCs, it is important to understand how the gene expression profile changes in SCs at different ages.MethodsHere, we usedSox2GFP/+mice to isolate the Sox2+ SCs at postnatal day (P)3, P7, P14, and P30 via flow cytometry. Next, we used RNA-seq to determine the transcriptome expression profiles of P3, P7, P14, and P30 SCs. To further analyze the relationships between these age-related and differentially expressed genes in Sox2+ SCs, we performed gene ontology (GO) analysis.ResultsConsistent with previous reports, we also found that the proliferation and HC regeneration ability of isolated Sox2+ SCs significantly decreased as mice aged. We identified numerous genes that are enriched and differentially expressed in Sox2+ SCs at four different postnatal ages, including cell cycle genes, signaling pathway genes, and transcription factors that might be involved in regulating the proliferation and HC differentiation ability of SCs. We thus present a set of genes that might regulate the proliferation and HC regeneration ability of SCs, and these might serve as potential new therapeutic targets for HC regeneration.ConclusionsIn our research, we found several genes that might play an important role in regulating the proliferation and HC regeneration ability of SCs. These datasets are expected to serve as a resource to provide potential new therapeutic targets for regulating the ability of SCs to regenerate HCs in postnatal mammals.
mTORC2 affects the maintenance of the muscle stem cell pool
Authors: Rion Nathalie , Castets Perrine , Lin Shuo , Enderle Leonie , Reinhard Judith R. , Rüegg Markus A. 
Published: December 2019

AbstractBackgroundThe mammalian target of rapamycin complex 2 (mTORC2), containing the essential protein rictor, regulates cellular metabolism and cytoskeletal organization by phosphorylating protein kinases, such as PKB/Akt, PKC, and SGK. Inactivation of mTORC2 signaling in adult skeletal muscle affects its metabolism, but not muscle morphology and function. However, the role of mTORC2 in adult muscle stem cells (MuSCs) has not been investigated.MethodUsing histological, biochemical, and molecular biological methods, we characterized the muscle phenotype of mice depleted for rictor in the Myf5-lineage (RImyfKO) and of mice depleted for rictor in skeletal muscle fibers (RImKO). The proliferative and myogenic potential of MuSCs was analyzed upon cardiotoxin-induced injury in vivo and in isolated myofibers in vitro.ResultsSkeletal muscle of young and 14-month-old RImyfKO mice appeared normal in composition and function. MuSCs from young RImyfKO mice exhibited a similar capacity to proliferate, differentiate, and fuse as controls. In contrast, the number of MuSCs was lower in young RImyfKO mice than in controls after two consecutive rounds of cardiotoxin-induced muscle regeneration. Similarly, the number of MuSCs in RImyfKO mice decreased with age, which correlated with a decline in the regenerative capacity of mutant muscle. Interestingly, reduction in the number of MuSCs was also observed in 14-month-old RImKO muscle.ConclusionsOur study shows that mTORC2 signaling is dispensable for myofiber formation, but contributes to the homeostasis of MuSCs. Loss of mTORC2 does not affect their myogenic function, but impairs the replenishment of MuSCs after repeated injuries and their maintenance during aging. These results point to an important role of mTORC2 signaling in MuSC for muscle homeostasis.
Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis
Authors: Zheng Ying , Gong Xun 
Published: December 2019

Abstract
Background
Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and community composition of microbiome associated with different plant compartments as well as bulk soils of cycad species remains elusive.

Method
An extensive investigation of species diversity and community composition of bacterial and fungal microbiome in roots, seeds, unfertilized seeds, ovules, pollens, and soils of Cycas panzhihuaensis L. Zhou & S. Y. Yang has been conducted by high-through sequencing technology. Moreover, principal component analysis (PCA), hierarchical cluster analysis (HCA), and heatmap analysis were applied to test the niche-specific effect and biogeography factor among different sample types of this cycad species.

Results
Highly diverse microbiota and significant variation of community structure were found among different compartments of C. panzhihuaensis. Soils exhibited a remarkable differentiation of bacterial community composition compared to the other five plant organs as revealed by PCA, HCA, and heatmap analyses. Different compartments possessed unique core microbial taxa with Pseudomonadaceae and Nectriaceae shared among them. According to the indicator species analysis, there was almost no differentiation of dominant microbiomes with regard to the geography of the host cycad. Two main transmission models existed in the C. panzhihuaensis.

Conclusions
Each sample type represented a unique niche and hosted a niche-specific core microbial taxa. Contrary to previous surveys, biogeography hardly exerted impact on microbial community variation in this study. The majority of the cycad-associated microbes were horizontally derived from soils and/or air environments with the rest vertically inherited from maternal plants via seeds. This study offers a robust knowledge of plant-microbiome interaction across various plant compartments and soils and lends guidelines to the investigation of adaptation mechanism of cycads in arid and nutrient-poor environments as well as their evolutionary conservation.
Facile aqueous-phase synthesis of Ag–Cu–Pt–Pd quadrometallic nanoparticles
Authors: Tang Zengmin , Yeo Byung Chul , Han Sang Soo , Lee Tae-Jin , Bhang Suk Ho , Kim Woo-Sik , Yu Taekyung 
Published: December 2019

AbstractAg–Cu–Pt–Pd quadrometallic nanoparticles which small Pt and Pd nanoparticles were attached on the surface of AgCu Janus nanoparticles were firstly synthesized by sequential reduction of Pt and Pd precursor in the presence of Janus AgCu bimetallic nanoparticles as seeds in an aqueous solution. Even though there was a small amount of Cu2O on the surface, the synthesized nanoparticles were mainly composed of four independent metallic part, not alloy parts. By theoretical calculation and growth mechanism study, we found that different reducing rate between Ag+ and Cu2+ and sequential reduction of Pt and Pd precursors would be key roles for the formation of the quadrometallic nanoparticles.
Metabolic pathway analysis for in silico design of efficient autotrophic production of advanced biofuels
Authors: Unrean Pornkamol , Tee Kang Lan , Wong Tuck Seng 
Published: December 2019

AbstractHerein, autotrophic metabolism ofCupriavidus necatorH16 growing on CO2, H2and O2gas mixture was analyzed by metabolic pathway analysis tools, specifically elementary mode analysis (EMA) and flux balance analysis (FBA). As case studies, recombinant strains ofC. necatorH16 for the production of short-chain (isobutanol) and long-chain (hexadecanol) alcohols were constructed and examined by a combined tools of EMA and FBA to comprehensively identify the cell’s metabolic flux profiles and its phenotypic spaces for the autotrophic production of recombinant products. The effect of genetic perturbations via gene deletion and overexpression on phenotypic space of the organism was simulated to improve strain performance for efficient bioconversion of CO2to products at high yield and high productivity. EMA identified multiple gene deletion together with controlling gas input composition to limit phenotypic space and push metabolic fluxes towards high product yield, while FBA identified target gene overexpression to debottleneck rate-limiting fluxes, hence pulling more fluxes to enhance production rate of the products. A combination of gene deletion and overexpression resulted in designed mutant strains with a predicted yield of 0.21–0.42 g/g for isobutanol and 0.20–0.34 g/g for hexadecanol from CO2. The in silico-designed mutants were also predicted to show high productivity of up to 38.4 mmol/cell-h for isobutanol and 9.1 mmol/cell-h for hexadecanol under autotrophic cultivation. The metabolic modeling and analysis presented in this study could potentially serve as a valuable guidance for future metabolic engineering ofC. necatorH16 for an efficient CO2-to-biofuels conversion.
Progressive cracking technique for phacoemulsification of superhard cataracts: a case report
Authors: Zhao Yun-e , Li Zhangliang , Chang Pingjun , Wang Dandan , Hu Man 
Published: December 2019

Abstract
Background
Complete nuclear disassembly of superhard cataracts cannot always be achieved by phaco chop, which is considered one of the best techniques for dealing with hard cataracts. We present a phaco chop-progressive cracking technique to divide superhard cataracts completely.

Case presentation
We presented a case of cataract with over Grade V nucleus sclerosis and very low density of corneal endothelial cell (812 cells/mm2). By performing the cataract surgery with our phaco chop-progressive cracking technique, the corneal endothelial cells were well protected and the patient’s visual acuity was markedly improved from finger counting at 40 cm to 20/200 the day after surgery without obvious corneal edema.

Conclusions
Although an initial learning curve was needed, this phaco chop-progressive cracking technique could be of particular benefit to the superhard cataract, especially in patients with low density of corneal endothelial cells.
A pilot study of the duration of GP consultations in Ireland
Authors: Pierse Tom , Barry Luke , Glynn Liam , Quinlan Diarmuid , Murphy Andrew , O’Neill Ciaran 
Published: December 2019

Abstract
Background
General practitioner (GP)-led primary care is the linchpin of health care in Ireland. Reflecting international trends, there are increasing concerns about the sustainability of the current Irish GP service due to an increasing workload. Objective data on the duration of GP consultations are currently not available in Ireland. The objective of this pilot study is to demonstrate how the duration of consultations can be collected, using readily available administrative data.

Methods
Software was developed to extract the duration of GP consultations using the opening and closing of electronic patient records associated with a GP consultation. GP practices (N = 3) comprising 15 GPs were recruited from a university-affiliated research network. A retrospective analysis of GP consultations with patients with diabetes for the 9 years between 2010 and 2018 was used to assess the feasibility of using this system to measure the duration of consultations.

Results
The average duration of a consultation was 14.1 min for the 9 years spanning 2010 to 2018. Patients had an average time between consultations of 99 days.

Conclusions
This pilot study confirms that an administrative data set can be utilised at negligible cost to monitor GP practice consultation workload over time. Our preliminary pilot data show that GP consultation durations among participating practices were longer than the 5–11.7 min reported in the UK and show an increase over the period. Clearly, a larger number of practices and patients are required to substantiate this finding.
UTI − quo vadis? New alternatives to treat uncomplicated urinary tract infections
Authors: Naber Kurt G. , Tandogdu Zafer , Köves Bela , Bonkat Gernot , Wagenlehner Florian 
Published: December 2019

AbstractUrinary tract infections (UTI) are one of the most common problems in urology clinics. The European Association of Urology (EAU) has been pioneering in its efforts to disseminate the latest clinical findings through the organization of the annual EAU congresses. At this year’s congress (EAU Barcelona 2019), various satellite symposia were organized, focusing on specific issues in the field of urology. "UTI − quo vadis? New alternatives to treat uncomplicated urinary tract infections" was one of the industry-sponsored symposia, organized with the aim of evaluating the current scenario and also throwing light on the paradigm shift in the treatment of acute, uncomplicated lower urinary tract infections (uUTI). Several interlinking topics were presented during this symposium. The topics covered antibiotic resistance, involving a presentation of the current data from the Global Prevalence Study on Infections in Urology (GPIU-study). This discussion was followed by case reports on the impact of antibiotic resistance on the management of patients with UTI/uUTI and treatment options for UTI/uUTI according to current guidelines. The highlight of the symposium was the presentation of very recent data from a gold standard phase III clinical trial (double-blind, double-dummy randomized study), demonstrating the non-inferiority of a herbal medicine (BNO 1045) versus antibiotic therapy (fosfomycin trometamol (FT), as a single dose = 3 g) for the treatment of acute, uncomplicated cystitis.
First record of the entomopathogenic protist, Mattesia dispora (Neogregarinorida: Lipotrophidae) of the Mediterranean flour moth, Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) in Turkey
Authors: Yaman Mustafa , Acar Kâbire Funda , Radek Renate 
Published: December 2019

AbstractThe present study is the first record of a natural neogregarine infection of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) in Turkey. The infection occurs in the fat body and hemolymph of the larvae. Typical fresh navicular oocysts of the pathogen were 12.1–16.2 μm in length and 5.9–8.5 in width (n = 50). Oocysts stained with Giemsa stain measured 11.7–14.2 μm in length and 5.9–8.5 μm in width. Polar plugs were recognizable using light and electron microscopy. The oocyst wall is quite thick, measuring 460 to 560 nm. Each oocyst contains 8 sporozoites. The described neogregarine has typical characteristics of members of the genus Mattesia (Family Lipotrophidaeorder Neogregarinorida) and shows similarities with Mattesia dispora in morphological and ultrastructural characteristics. The occurrence of the pathogen in different life stages of E. kuehniella was also studied. Total infection was observed as 66.98% in the investigated samples. The pathogen caused different infection levels in the larvae, pupae, and adults of the E. kuehniella, 57.06, 85, and 3.17%, respectively.
Policing in Practice
Authors: Ibrahim Farhana 
Published: December 2019

AbstractStudies on militarization and borders in South Asia often focus on zones of spectacular conflict, such as Kashmir, or partition violence in Punjab. This article examines the production of everyday policing in a zone of high surveillance that is not a conventional military “hot spot” in the region. The question of who or what constitutes the police force is as important as the question of what it does. The categories of police or law enforcer and those who are policed are malleable and contingent. Networks of secrecy, transparency, and trust are produced through a series of dialogic relationships between police, borderland residents, and other actors not conventionally taken to be a part of the security apparatus—for example, tourists, development agencies, and anthropologists. The article suggests that encounters between those on either side of the law are not only coercive, but shot through with shades of hospitality, reciprocity, and desire. It thus attempts to refigure wartime and peacetime as periods of continuum rather than opposition and repositions those who are inside and outside formal categories of law enforcement to suggest that the manner in which the border is policed may reflect the ways in which borderland populations are engaged quite actively with the question of security.
Security Socialities
Authors: Ghosh Sahana 
Published: December 2019

Abstract
India imposes an increasingly militarized border security agenda along its officially “friendly” border with Bangladesh with a range of preemptive practices to control the illegal movement of people and goods. Focusing ethnographic attention on everyday mobility, I view the articulations of national security in India's eastern borderlands through a gender lens to trace the logics of threat and protection that are made and unmade in everyday civil-military relations. The article explores the social and spatial forms through which civil-military relations unfold and proposes the idea of “security socialities” to think about these polychromatic relations between residents and security force personnel. Intimate yet fluid, ambivalent, and potentially violent, these instantiations of power show how border security is concretized and negotiated, stretched and challenged, but also made acceptable for a range of borderland residents. Security socialities point to the inextricable ties between everyday and spectacular violence of security projects and the relations that constitute them.
The Social Life of Rumors
Authors: Maqsood Ammara 
Published: December 2019

Abstract
In the aftermath of 9/11, with respect to the US-led invasion of Afghanistan, the Federally Administered Tribal Areas (FATA) in Pakistan have been the site of immense violence and destruction, including from US drone attacks, ground military operations by the Pakistan Army, and retaliatory attacks by different factions of Taliban fighters. Using uncertainty as an analytic and ethnographic concept, this article traces the social life of the rumors, conspiracy theories, and stories that float around this violence. It draws attention to their multiple and often contradictory effects: rumors simultaneously breed fear and confusion, help forge intimacy, and provide certainty and coherence. Rather than subvert power relations or simply critique the powerful, I suggest that rumors and conspiracy theories provide the means through which tribal Pashtuns live and make their way in a social world in which they remain unequal, but coeval, participants.
Afterword
Authors: Feldman Ilana 
Published: December 2019

Abstract
This brief essay reflects on a collection of anthropological investigations of security and surveillance practices in South Asia and the Middle East. The articles in the collection highlight what looking at security matters reveals about families, migration, borderland experiences, and ethnographic fieldwork. The afterword considers the intellectual and ethical importance of the ethnographic sensitivity to and analytic engagement with the uncertainties and ambiguities that are at the center of these practices. Individually and collectively, the articles in this collection offer new tools for thinking about the effects of living in securitized worlds and underscore the value of looking from perhaps unexpected vantage points to understand an arguably global condition.
Nanog regulates Pou3f1 expression at the exit from pluripotency during gastrulation
Authors: Barral Antonio , Rollan Isabel , Sanchez-Iranzo Hector , Jawaid Wajid , Badia-Careaga Claudio , Menchero Sergio , Gomez Manuel J. , Torroja Carlos , Sanchez-Cabo Fatima , Göttgens Berthold , Manzanares Miguel , Sainz de Aja Julio 
Published: December 2019

ABSTRACT
Pluripotency is regulated by a network of transcription factors that maintain early embryonic cells in an undifferentiated state while allowing them to proliferate. NANOG is a critical factor for maintaining pluripotency and its role in primordial germ cell differentiation has been well described. However, Nanog is expressed during gastrulation across all the posterior epiblast, and only later in development is its expression restricted to primordial germ cells. In this work, we unveiled a previously unknown mechanism by which Nanog specifically represses genes involved in anterior epiblast lineage. Analysis of transcriptional data from both embryonic stem cells and gastrulating mouse embryos revealed Pou3f1 expression to be negatively correlated with that of Nanog during the early stages of differentiation. We have functionally demonstrated Pou3f1 to be a direct target of NANOG by using a dual transgene system for the controlled expression of Nanog. Use of Nanog null ES cells further demonstrated a role for Nanog in repressing a subset of anterior neural genes. Deletion of a NANOG binding site (BS) located nine kilobases downstream of the transcription start site of Pou3f1 revealed this BS to have a specific role in the regionalization of the expression of this gene in the embryo. Our results indicate an active role of Nanog inhibiting neural regulatory networks by repressing Pou3f1 at the onset of gastrulation.
This article has an associated First Person interview with the joint first authors of the paper.
Impact on Health-Related Quality of Life of Video-Assisted Thoracoscopic Surgery for Lung Cancer
Authors: Avery Kerry N. L. , Blazeby Jane M. , Chalmers Katy A. , Batchelor Timothy J. P. , Casali Gianluca , Internullo Eveline , Krishnadas Rakesh , Evans Clare , West Doug 
Published: December 2019

Abstract
Background
Video-assisted thoracoscopic surgery (VATS) approaches are increasingly used in lung cancer surgery, but little is known about their impact on patients’ health-related quality of life (HRQL). This prospective study measured recovery and HRQL in the year after VATS for non-small cell lung cancer (NSCLC) and explored the feasibility of HRQL data collection in patients undergoing VATS or open lung resection.

Patients and Methods
Consecutive patients referred for surgical assessment (VATS or open surgery) for proven/suspected NSCLC completed HRQL and fatigue assessments before and 1, 3, 6 and 12 months post-surgery. Mean HRQL scores were calculated for patients who underwent VATS (segmental, wedge or lobectomy resection). Paired t-tests compared mean HRQL between baseline and expected worst (1 month), early (3 months) and longer-term (12 months) recovery time points.

Results
A total of 92 patients received VATS, and 18 open surgery. Questionnaire response rates were high (pre-surgery 96–100%; follow-up 67–85%). Pre-surgery, VATS patients reported mostly high (good) functional health scores [(European Organisation for Research and Treatment of Cancer) EORTC function scores > 80] and low (mild) symptom scores (EORTC symptom scores < 20). One-month post-surgery, patients reported clinically and statistically significant deterioration in overall health and physical, role and social function (19–36 points), and increased fatigue, pain, dyspnoea, appetite loss and constipation [EORTC 12–26; multidimensional fatigue inventory (MFI-20) 3–5]. HRQL had not fully recovered 12 months post-surgery, with reduced physical, role and social function (10–14) and persistent fatigue and dyspnoea (EORTC 12–22; MFI-20 2.7–3.2).

Conclusions
Lung resection has a considerable detrimental impact on patients’ HRQL that is not fully resolved 12 months post-surgery, despite a VATS approach.

Graphic Abstract