bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of human pluripotent stem cells into kidney tissues by synthetic mRNAs encoding transcription factors
Authors: Hiratsuka Ken , Monkawa Toshiaki , Akiyama Tomohiko , Nakatake Yuhki , Oda Mayumi , Goparaju Sravan Kumar , Kimura Hiromi , Chikazawa-Nohtomi Nana , Sato Saeko , Ishiguro Keiichiro , Yamaguchi Shintaro , Suzuki Sayuri , Morizane Ryuji , Ko Shigeru B. H. , Itoh Hiroshi , Ko Minoru S. H. 
Published: January 2019

AbstractThe derivation of kidney tissues from human pluripotent stem cells (hPSCs) and its application for replacement therapy in end-stage renal disease have been widely discussed. Here we report that consecutive transfections of two sets of synthetic mRNAs encoding transcription factors can induce rapid and efficient differentiation of hPSCs into kidney tissues, termed induced nephron-like organoids (iNephLOs). The first set - FIGLA, PITX2, ASCL1 and TFAP2C, differentiated hPSCs into SIX2+SALL1+ nephron progenitor cells with 92% efficiency within 2 days. Subsequently, the second set - HNF1A, GATA3, GATA1 and EMX2, differentiated these cells into PAX8+LHX1+ pretubular aggregates in another 2 days. Further culture in both 2-dimensional and 3-dimensional conditions produced iNephLOs containing cells characterized as podocytes, proximal tubules, and distal tubules in an additional 10 days. Global gene expression profiles showed similarities between iNephLOs and the human adult kidney, suggesting possible uses of iNephLOs as in vitro models for kidneys.
New insights into culture negative endophthalmitis by unbiased next generation sequencing
Authors: Deshmukh Dhanshree , Joseph Joveeta , Chakrabarti Moumita , Sharma Savitri , Jayasudha Rajagopalaboopathi , Sama Kalyana C. , Sontam Bhavani , Tyagi Mudit , Narayanan Raja , Shivaji S. 
Published: January 2019

AbstractThe proof-of-concept, study to investigate the presence of microorganisms in presumed infectious endophthalmitis using Next generation sequencing (NGS) was carried out in vitreous biopsies from 34 patients with endophthalmitis, and thirty patients undergoing surgery for non-infectious retinal disorders as controls. Following DNA extraction using the Qiagen mini kit and PCR amplification of the V3–V4 regions of the bacterial 16S rRNA and ITS 2 region of fungus, they samples were sequenced on an Illumina HiSeq 2500 Machine. Paired reads were curated, taxonomically labeled, and filtered. Culture based diagnosis was achieved in 15/34 (44%) patients while NGS diagnosed the presence of microbes in 30/34 (88%) patients (bacteria in 26/30, fungi in 2/30, mixed infections in 2/30 cases). All 30 controls were negative for bacteria or fungus by NGS. There was good agreement between culture and NGS for culture-positive cases. Among culture negative cases, DNA of common culturable bacteria were identified like Streptococcus sp., Staphylococcus sp., Pseudomonas sp., Gemella sp., Haemophilus sp., Acinetobacter sp. The specificity of NGS with culture and clinical diagnosis was found to be 20% and 100% respectively and sensitivity of NGS with culture and clinical diagnosis was found to be 87.5% and 88% respectively. NGS appears to be promising diagnostic platform for the diagnosis of infectious culture negative endophthalmitis.
Survey of the bacteriophage phoH gene in wetland sediments in northeast China
Authors: Li Xiang , Sun Yan , Liu Junjie , Yao Qin , Wang Guanghua 
Published: January 2019

AbstractPhoH is a host-derived auxiliary metabolic gene that can be used as a new biomarker for surveying phage diversity in marine and paddy waters. However, the applicability of this gene in other environments has not been addressed. In this paper, we surveyed the phoH gene in four wetland sediments in northeast China. DNA was extracted directly from sediments and used for PCR amplification with the degenerate primers vPhoHf and vPhoHr. In total, 44 and 58 phoH sequences were identified as belonging to bacteria and phages, respectively, suggesting that this primer set is not highly specific to the phage phoH gene. A BLASTp search showed that the 58 phage phoH sequences had the highest identity to the known viral sequences, ranging from 48% to 100%. Phylogenetic analysis showed that all phage sequences from wetlands distributed into the previously designated Groups 2, 3, 4 and 6. In addition, two new subgroups, Groups 2c and 4c, which contained sequences exclusively from wetlands, were detected in this study. Nonmetric multidimensional scaling analysis showed that the phage phoH assemblage from a coastal wetland was similar to that in marine environments, while the phage phoH assemblage from a lake wetland was similar to that in paddy waters. These findings indicated that different types of wetlands had distinct phage phoH compositions.
Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile
Authors: Carlucci Christian , Jones Carys S. , Oliphant Kaitlyn , Yen Sandi , Daigneault Michelle , Carriero Charley , Robinson Avery , Petrof Elaine O. , Weese J. Scott , Allen-Vercoe Emma 
Published: January 2019

AbstractMany cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
Hyperautofluorescent Dots are Characteristic in Ceramide Kinase Like-associated Retinal Degeneration
Authors: Sengillo Jesse D. , Cho Galaxy Y. , Paavo Maarjaliis , Lee Winston , White Eugenia , Jauregui Ruben , Sparrow Janet R. , Allikmets Rando , Tsang Stephen H. 
Published: January 2019

AbstractThere is a lack of studies which seek to discern disease expression in patients with mutations that alter retinal ceramide metabolism, specifically in the ceramide kinase like (CERKL) gene. This cross-sectional case series reports a novel phenotypic manifestation of CERKL-associated retinopathy. Four unrelated patients with homozygous CERKL mutations underwent a complete ocular exam, spectral-domain optical coherence tomography, short-wavelength fundus autofluorescence (SW-AF), quantitative autofluorescence (qAF), and full-field electroretinogram (ffERG). Decreased visual acuity and early-onset maculopathy were present in all patients. All four patients had extensive hyperautofluorescent foci surrounding an area of central atrophy on SW-AF imaging, which has not been previously characterized. An abnormal spatial distribution of qAF signal was seen in one patient, and abnormally elevated qAF8 signal in another patient. FfERG recordings showed markedly attenuated rod and cone response in all patients. We conclude that these patients exhibit several features that, collectively, may warrant screening of CERKL as a first candidate: early-onset maculopathy, severe generalized retinal dysfunction, peripheral lacunae, intraretinal pigment migration, and hyperautofluorescent foci on SW-AF.
Pharmacological cholesterol depletion disturbs ciliogenesis and ciliary function in developing zebrafish
Authors: Maerz Lars D. , Burkhalter Martin D. , Schilpp Carolin , Wittekindt Oliver H. , Frick Manfred , Philipp Melanie 
Published: January 2019

AbstractPatients with an inherited inability to synthesize sufficient amounts of cholesterol develop congenital malformations of the skull, toes, kidney and heart. As development of these structures depends on functional cilia we investigated whether cholesterol regulates ciliogenesis through inhibition of hydroxymethylglutaryl-Coenzyme A reductase (HMG-CoA-R), the rate-limiting enzyme in cholesterol synthesis. HMG-CoA-R is efficiently inhibited by statins, a standard medication for hyperlipidemia. When zebrafish embryos are treated with statins cilia dysfunction phenotypes including heart defects, left-right asymmetry defects and malformation of ciliated organs develop, which are ameliorated by cholesterol replenishment. HMG-CoA-R inhibition and other means of cholesterol reduction lowered ciliation frequency and cilia length in zebrafish as well as several mammalian cell types. Cholesterol depletion further triggers an inability for ciliary signalling. Because of a reduction of the transition zone component Pi(4,5)P2 we propose that cholesterol governs crucial steps of cilium extension. Taken together, we report that cholesterol abrogation provokes cilia defects.
Direct manipulation of liquid ordered lipid membrane domains using optical traps
Authors: Friddin Mark S. , Bolognesi Guido , Salehi-Reyhani Ali , Ces Oscar , Elani Yuval 
Published: January 2019

AbstractMulticomponent lipid bilayers can give rise to coexisting liquid domains that are thought to influence a host of cellular activities. There currently exists no method to directly manipulate such domains, hampering our understanding of their significance. Here we report a system that allows individual liquid ordered domains that exist in a liquid disordered matrix to be directly manipulated using optical tweezers. This allows us to drag domains across the membrane surface of giant vesicles that are adhered to a glass surface, enabling domain location to be defined with spatiotemporal control. We can also use the laser to select individual vesicles in a population to undergo mixing/demixing by locally heating the membrane through the miscibility transition, demonstrating a further layer of control. This technology has potential as a tool to shed light on domain biophysics, on their role in biology, and in sculpting membrane assemblies with user-defined membrane patterning.
Team Approach for Education and Support of Postoperative Pediatric Cerebellar Mutism Syndrome in the Preoperative and Immediately Postoperative Phase
Authors: Molinaro Laura Hinkes , Stellpflug Wendy 
Published: January 2019

Purpose
Postoperative pediatric cerebellar mutism syndrome (CMS) is a known complication following surgical resection of posterior fossa tumors. However, minimal information exists describing the progression of the syndrome and how to best support these patients. At Ann & Robert H. Lure Children's Hospital of Chicago, the brain tumor team has been fortunate enough to work together for years. Throughout the time that this particular team has been collaborating, a typical protocol has been developed for children at most risk for postoperative pediatric CMS, refined with each patient experience, to the current model. Much of what has been written about postoperative pediatric CMS (and varying terminology) has focused on potential risk factors, surgical approach, and causes, as well as definitively defining the syndrome. We would like to focus on the impact the mutism has on this constellation of symptoms. We would like to focus on the patient and family and how we as caregivers can prepare, educate, and support the family throughout this difficult diagnosis and early management of mutism.

Conclusions
There is much work to be done in describing and quantifying postoperative pediatric CMS. In the care of children with pediatric brain tumors in the preoperative and immediately postoperative phase, a team approach is paramount. When discussing expectations following surgery, consistent message and communication of hope are essential.
Dispelling the Myth of Work-Related de Quervain's Tenosynovitis
Authors: Dunn John , Polmear Michael , Nesti Leon 
Published: January 2019

AbstractDe Quervain’s Tenosynovitis (DQT) is a common condition characterized by pain about the dorsal-radial aspect of the wrist, just proximal to the radial styloid. The condition is precipitated by a thickened first dorsal compartment and its tendons. The impression that DQT is caused from work-related injury is misdirected, as no study has established an association between hand usage at work or trauma with DQT. Physicians should exercise caution when discussing the causes and natural history of DQT with symptomatic patients.
Inositol polyphosphate multikinase mediates extinction of fear memory
Authors: Park Jina , Longo Francesco , Park Seung Ju , Lee Seulgi , Bae Mihyun , Tyagi Richa , Han Jin-Hee , Kim Seyun , Santini Emanuela , Klann Eric , Snyder Solomon H. 
Published: January 2019

Significance
Inositol polyphosphate multikinase (IPMK) is a pleiotropic enzyme for the biosynthesis of inositol polyphosphates and phosphatidylinositol 3,4,5-trisphosphate, but the neural function of IPMK has remained largely elusive. By conditionally deleting IPMK from the excitatory neurons of the postnatal forebrain in mice, we found that IPMK knockout mice exhibited normal cued fear conditioning but showed enhanced fear extinction accompanied by selective activation of p85 S6 kinase 1 in the IPMK-null amygdala following fear extinction. Electrophysiological recording analyses further uncovered facilitated hippocampal long-term potentiation from IPMK knockout mice. Thus, our data propose IPMK as a molecular player in the control of fear extinction.
Stratification of reactivity determines nitrate removal in groundwater
Authors: Kolbe Tamara , de Dreuzy Jean-Raynald , Abbott Benjamin W. , Aquilina Luc , Babey Tristan , Green Christopher T. , Fleckenstein Jan H. , Labasque Thierry , Laverman Anniet M. , Marçais Jean , Peiffer Stefan , Thomas Zahra , Pinay Gilles 
Published: January 2019

Significance
Although groundwater is a critical source of drinking water and irrigation, it has been polluted worldwide by agriculture, industry, and domestic activity. Because assessing groundwater quality and recovery rates is challenging, we developed a method for determining where and how quickly nitrate is removed in aquifers using just a few point measurements of groundwater chemistry. This methodology opens new avenues for characterizing catchment-scale nutrient dynamics, including nitrogen, carbon, and silica, with existing datasets for ecosystems around the globe. Understanding the subsurface structure of reactivity would also improve estimates of recovery time frames for polluted ecosystems and inform sustainable limits for anthropogenic activity.
Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis
Authors: Wilharm Anneke , Tabib Yaara , Nassar Maria , Reinhardt Annika , Mizraji Gabriel , Sandrock Inga , Heyman Oded , Barros-Martins Joana , Aizenbud Yuval , Khalaileh Abed , Eli-Berchoer Luba , Elinav Eran , Wilensky Asaf , Förster Reinhold , Bercovier Herve , Prinz Immo , Hovav Avi-Hai 
Published: January 2019

Significance
Elucidating the mechanisms by which homeostasis is established and maintained in the oral mucosa is important for human health. In this study we investigated the ontogeny and function of gingival γδT cells. The majority of these cells originate from embryonic precursors that maintain themselves locally independent of circulating γδT cells arising from adult precursors. The oral microbiota regulates the development of γδT cells, particularly those of embryonic origin. γδT cells represent the major sources of IL-17–producing cells in the gingiva, and they play a critical role in down-modulating gingival steady-state immunity that subsequently shapes oral microbial diversity. This suggests that oral homeostasis requires mutual interactions between γδT cells and the microbiota.
PMC text mining subset in BioC: about three million full-text articles and growing
Authors: Comeau Donald C , Wei Chih-Hsuan , Islamaj Doğan Rezarta , Lu Zhiyong 
Published: January 2019

Abstract

Motivation
Interest in text mining full-text biomedical research articles is growing. To facilitate automated processing of nearly 3 million full-text articles (in PubMed Central® Open Access and Author Manuscript subsets) and to improve interoperability, we convert these articles to BioC, a community-driven simple data structure in either XML or JavaScript Object Notation format for conveniently sharing text and annotations.

Results
The resultant articles can be downloaded via both File Transfer Protocol for bulk access and a Web API for updates or a more focused collection. Since the availability of the Web API in 2017, our BioC collection has been widely used by the research community.

Availability and implementation
https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/.
Multicentre experience with two frozen elephant trunk prostheses in the treatment of acute aortic dissection†
Authors: Berger Tim , Weiss Gabriel , Voetsch Andreas , Arnold Zsuzsanna , Kreibich Maximilian , Rylski Bartosz , Krombholz-Reindl Philipp , Winkler Andreas , Mach Markus , Geisler Daniela , Seitelberger Rainald , Siepe Mathias , Beyersdorf Friedhelm , Grabenwoeger Martin , Czerny Martin , Gottardi Roman 
Published: January 2019

Abstract

OBJECTIVES
The aim of this study was to evaluate early- and mid-term outcome and aortic remodelling in patients undergoing implantation of 2 different frozen elephant trunk prostheses, either the Thoraflex™ hybrid (Vascutek, Inchinnan, UK) and the E-vita Open (Jotec Inc., Hechingen, Germany) for acute aortic dissection.

METHODS
All consecutive patients [n = 88; median age 59 (49–67) years; 69% male] undergoing surgery with a frozen elephant trunk prosthesis for acute aortic dissection from August 2005 until March 2018 were included in this study. The Thoraflex™ device was implanted in 55 patients and the E-vita Open graft in 33 patients.

RESULTS
Preoperative characteristics did not differ significantly between groups. There was also no statistically significant difference in postoperative outcome: in-hospital mortality (11% vs 12%; P > 0.99), stroke (18% vs 6%; P = 0.12) and spinal cord injury (6% vs 6%; P > 0.99). While there was no statistically significant difference in the occurrence of distal stent graft-induced new entries (16% vs 18%; P = 0.77), there was a significantly higher rate of secondary endovascular aortic interventions in the Thoraflex™ hybrid group (22% vs 0%; P = 0.003). There was a trend towards a higher rate of false lumen thrombosis at the level of the stent graft (74% vs 95%; P = 0.085) and was comparable at the thoraco-abdominal transition (53% vs 80%; P = 0.36) 1 year after implantation of the prostheses.

CONCLUSIONS
In this comparison of 2 frozen elephant trunk prostheses, there is no evidence that different surgical techniques influence in-hospital outcome. At 1-year follow-up, patients who underwent implantation of the E-vita Open prosthesis showed a significantly reduced rate of secondary aortic interventions and a trend towards a higher rate of false lumen thrombosis which might be attributed to a longer coverage of the descending aorta due to a longer stent graft design and significantly more frequent implantation in zone 3.
Behavioural disorders in children with pectus excavatum in China: a retrospective cohort study with propensity score matching and risk prediction model
Authors: Li Hongbo , Jin Xianqing , Fan Shulei , Wang Daoxin , Wu Chun , Pan Zhengxia , Li Yonggang , An Yong , Wang Gang , Dai Jiangtao , Wang Quan 
Published: January 2019

Abstract

OBJECTIVES
Surgical repair of pectus excavatum is typically carried out immediately prior to puberty. However, at the time of surgery, some psychosocial issues, such as behavioural disorders may already have developed and the likelihood of these psychosocial disorders resolving after surgery is unclear. For this reason, some surgeons choose to perform surgical repair at an earlier age in some children. The study retrospectively compares the rate of behavioural disorders in children undergoing the Nuss procedure at 4 vs. 10 years of age. We also attempted to develop a model to predict the risk of behavioural disorders in 10 year-old patients.

METHODS
The current study included children receiving Nuss procedure for pectus excavatum at either 4 or 10 years of age. The presence/absence of behavioural disorder was assessed preoperatively, and in the third year, after removal of the bar. A propensity score matching (PSM) analysis was conducted to reduce the potential for confounding by baseline factors. Multivariable logistic regression was conducted to establish a model to predict the risk of behavioural disorders in the third year after the removal of the bar. The model was accessed by discrimination and calibration. A formula and a nomogram were developed based on the results.

RESULTS
The number of patients in each group was 45 after PSM. The rate of behavioural disorders at the baseline was significantly higher in the children undergoing Nuss procedure at 10 years of age [36% vs 20%, odds ratio (OR) 2.21, 95% confidence interval (CI) 0.85–5.72; P = 0.157]. The rate of behavioural disorders in the third year after the removal of the bar was 36% and 18% in children undergoing surgery at 10 and 4 years of age, respectively (OR 2.55, 95% CI 0.96–6.79; P = 0.094). The rate of persistent behavioural disorders, defined as continuing to have behavioural disorders in the third year after the removal of the bar in those with behavioural disorders at the baseline, was 88% vs 56% (OR 3.47, 95% CI 0.56–21.36; P = 0.204). Two patients (4%) relapsed in each group. A risk prediction model by variables of gender, Haller index, pulmonary function and score of Child Behaviour Checklist at the baseline was provided.

CONCLUSIONS
The rate of behavioural disorders was considerably lower in children who underwent the Nuss procedure at 4 years of age than at 10 years of age. Behavioural disorders may not readily resolve after surgery. Performing surgery at an early age rather than just before puberty may be better for psychosocial development. Psychosocial aid is necessary in addition to surgery to address behavioural disorders.