bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic background of the Klebsiella pneumoniae NDM-1 outbreak in Poland, 2012–18
Authors: Izdebski R , Sitkiewicz M , Urbanowicz P , Krawczyk M , Brisse S , Gniadkowski M 
Published: July 2020

Abstract

Objectives
To characterize genomes of Klebsiella pneumoniae ST11 NDM-1 responsible for a countrywide outbreak in Poland and compare them phylogenetically with other Polish and international ST11 strains.

Methods
Seventy-one carbapenemase-producing K. pneumoniae ST11 isolates from Poland, including 66 representatives of the NDM-1 epidemic from 2012–18, were sequenced using Illumina MiSeq. Additionally, three outbreak isolates were also sequenced using MinION. The clonality and phylogenetic analysis was done by core-genome MLST and SNP approaches. Resistomes, virulomes, K/O antigens and plasmid replicons were screened for. The detailed plasmid analysis was based on full assemblies using Oxford Nanopore Technologies data.

Results
Chromosomes of the outbreak isolates formed an essentially homogeneous cluster (though accumulating SNPs gradually with time), differing remarkably from other Polish NDM-1/-5-, KPC-2- or OXA-48-producing K. pneumoniae ST11 strains. The cluster belonged to a clade with 72 additional isolates identified worldwide, including closely related NDM-1 producers from several countries, including organisms from Bulgaria and Greece. All these had KL24 and O2v1 antigens and the chromosomal yersiniabactin locus YbST230 residing in the ICEKp11 element. The specific blaNDM-1-carrying Tn125 transposon derivative, named Tn125A, was located in IncFII/pKPX-1- and/or IncR-like plasmids; however, the IncRs rearranged extensively during the outbreak, contributing to highly dynamic plasmid profiles and resistomes.

Conclusions
The K. pneumoniae ST11 NDM-1 genotype that has been expanding in Poland since 2012 is largely monoclonal and represents a novel international high-risk lineage that is also spreading in other countries.
A Shared Diagnostic Stewardship Approach toward Improving Autoimmune Encephalopathy Send-out Testing Utilization
Authors: Sharp Cierra N , Fletcher Anita , Muluhngwi Penn , Snyder James , Linder Mark W , Jortani Saeed A 
Published: July 2020

Abstract

Background
For many laboratories, autoimmune encephalopathy (AE) panels are send-out tests. These tests are expensive, and ordering patterns vary greatly. There is also a lack of consensus on which panel to order and poor understanding of the clinical utility of these panels. These challenges were presented to our newly formed, multidisciplinary, diagnostic stewardship committee (DSC). Through this collaboration, we developed an algorithm for ordering AE panels; combining diagnostic criteria with practice guidelines.

Methods
We analyzed test-ordering patterns in 2018 and calculated a true-positive rate based on clinical presentation and panel interpretation. An evidence-based approach was combined with input from the Department of Neurology to synthesize our algorithm. Efficacy of the algorithm (number of panels ordered, cost, and true positives) was assessed before and after implementation.

Results
In 2018, 77 AE-related panels were ordered, costing $137 510. The true-positive rate was 10%, although ordering multiple, similar panels for the same patient was common. Before implementing the algorithm (January 1–July 31, 2019), 55 panels were ordered, costing $105 120. The total true-positive rate was 3.6%. After implementation, 23 tests were ordered in a 5-month period, totaling $50 220. The true-positive rate was 13%.

Conclusion
With the DSC-directed mandate, we developed an algorithm for ordering AE panels. Comparison of pre- and postimplementation data showed a higher true-positive rate, indicating that our algorithm was able to successfully identify the at-risk population for AE disorders. This was met with a 43% decrease in the number of tests ordered, with total cost savings of $25 000 over 5 months.
Influence of climate change on the predicted distributions of the genus Tympanoctomys (Rodentia, Hystricomorpha, Octodontidae), and their conservation implications
Authors: Tarquino-Carbonell A P , Ojeda Ricardo A , Ojeda Agustina A 
Published: July 2020

Abstract
Viscacha rats (genus Tympanoctomys Yepes, 1942) are ecologically, physiologically, and behaviorally unusual octodontid rodents endemic to the Monte and Patagonian desert biomes of Argentina. The geographic ranges of the different species of Tympanoctomys have been described in general terms but have not been associated with spatial and climate data. Within species, populations are patchily distributed and genetically distinct. We investigated the predicted distribution of Tympanoctomys and the influence of climate fluctuations on their geographic range in historical, current, and future, scenarios. Our objectives were to characterize the environmental niche of the genus, propose a paleoclimatic context for the oldest fossils, characterize the environmental niches for T. barrerae and T. kirchnerorum, and forecast potential future distributions for these taxa. Ecological niche models were constructed using occurrence records from 1941 to the present wherein we identified several precipitation and temperature variables as important predictors of the geographic distributions of the genus, and the species T. barrerae and T. kirchnerorum. Based on our models’ results, we hypothesize that the distribution of Tympanoctomys has contracted from historical to modern times. At the species level, T. kirchnerorum likely experienced the most dramatic change, suffering a large contraction of its historical distribution resulting in its limited present distribution. Given these findings, projected future climate fluctuations and global warming are expected to affect the distributions and persistence of these species.
Population genetic structures at multiple spatial scales: importance of social groups in European badgers
Authors: Jacquier Mickaël , Vandel Jean-Michel , Léger François , Duhayer Jeanne , Pardonnet Sylvia , Queney Guillaume , Kaerle Cécile , Say Ludovic , Ruette Sandrine , Devillard Sébastien 
Published: July 2020

AbstractPopulation viability and metapopulation dynamics are strongly affected by gene flow. Identifying ecological correlates of genetic structure and gene flow in wild populations is therefore a major issue both in evolutionary ecology and species management. Studying the genetic structure of populations also enables identification of the spatial scale at which most gene flow occurs, hence the scale of the functional connectivity, which is of paramount importance for species ecology. In this study, we examined the genetic structure of a social, continuously distributed mammal, the European badger (Meles meles), both at large spatial scales (among populations) and fine (within populations) spatial scales. The study was carried out in 11 sites across France utilizing a noninvasive hair trapping protocol at 206 monitored setts. We identified 264 badgers genotyped at 24 microsatellite DNA loci. At the large scale, we observed high and significant genetic differentiation among populations (global Fst = 0.139; range of pairwise Fst [0.046–0.231]) that was not related to the geographic distance among sites, suggesting few large-scale dispersal events. Within populations, we detected a threshold value below which badgers were genetically close (&lt; 400 m), highlighting that sociality is the major structuring process within badger populations at the fine scale.
Doubling Down: Zechariah’s Oracle, Judah’s Blessing, and the Triumphal Entry in Matthew
Authors: Ferda Tucker S 
Published: July 2020

Abstract
For centuries exegetes have struggled to explain why Matthew presents two animals in the triumphal entry—a female ὄνος and her πῶλος—while all the other Gospels only have one (a πῶλος). The question is further complicated by the fact that the Scripture Matthew cites as fulfilled in this action—Zech. 9:9—also presents only one animal in all extant versions. So what is the historical or exegetical reason for Matthew’s addition? While many have argued that Matthew’s presentation stems from a misreading of the poetic parallelism in Zech. 9:9, this essay contends that Matthew’s doubling of Mark’s single πῶλος is the result of messianic exegesis. The argument is that Matthew or Matthew’s tradition has read Zech. 9:9 alongside another famous messianic oracle, Jacob’s blessing of Judah in Gen. 49:10–11, and that the doubling of the donkeys stems from a likely mistaken—though completely understandable—reading of the Hebrew text. The essay further shows that Matthew’s use of Gen. 49 and Zech. 9 in the triumphal entry scene makes good sense in light of the interests of the Gospel as a whole as well as exegetical tradition that stems from these passages.
Eccentric grazing envelope evolution towards Type IIb supernova progenitors
Authors: Shishkin Dmitry , Soker Noam 
Published: July 2020

ABSTRACT
We simulate the evolution of eccentric binary systems in the frame of the grazing envelope evolution (GEE) channel for the formation of Type IIb supernovae (SNe IIb), and find that extra mass removal by jets increases the parameter space for the formation of SNe IIb in this channel. To explore the role of eccentricity and the extra mass removal by jets, we use the stellar evolutionary code mesa binary. The initial primary and secondary masses are M1, i = 15 and M2, i = 2.5 M⊙. We examine initial semimajor axes of 600–1000 R⊙, and eccentricities of e = 0–0.9. Both Roche lobe overflow (RLOF) and mass removal by jets, followed by a wind, leave a hydrogen mass in the exploding star of MH, f ≈ 0.05 M⊙, compatible with an SN IIb progenitor. When the initial orbit is not circular, the final orbit might have a very high eccentricity. In many cases, with and without the extra mass removal by jets, the system can enter a common envelope evolution (CEE) phase, and then gets out from it. For some ranges of eccentricities, the jets are more efficient in preventing the CEE. Despite the large uncertainties, extra mass removal by jets substantially increases the likelihood of the system to get out from a CEE. This strengthens earlier conclusions for circular orbits. In some cases, RLOF alone, without mass removal by jets, can form SN IIb progenitors. We estimate that the extra mass removal by jets in the GEE channel increases the number of progenitors relative to that by RLOF alone by about a factor of 2.
Dissecting the regions around IceCube high-energy neutrinos: growing evidence for the blazar connection
Authors: Giommi P , Glauch T , Padovani P , Resconi E , Turcati A , Chang Y L 
Published: July 2020

ABSTRACT
The association of two IceCube detections, the IceCube-170922A event and a neutrino flare, with the blazar TXS 0506+056, has paved the way for the multimessenger quest for cosmic accelerators. IceCube has observed many other neutrinos but their origin remains unknown. To better understand the reason for the apparent lack of neutrino counterparts, we have extended the comprehensive dissection of the sky area performed for the IceCube-170922A event to all 70 public IceCube high-energy neutrinos that are well reconstructed and off the Galactic plane. Using the multifrequency data available through the Open Universe platform, we have identified numerous candidate counterparts of IceCube events. We report here the classification of all the γ-ray blazars found and the results of subsequent statistical tests. In addition, we have checked the 4LAC, 3FHL, and 3HSP catalogues for potential counterparts. Following the dissection of all areas associated with IceCube neutrinos, we evaluate the data using a likelihood-ratio test and find a $3.23\, \sigma$ (post-trial) excess of HBLs and IBLs with a best fit of 15 ± 3.6 signal sources. This result, together with previous findings, consistently points to a growing evidence for a connection between IceCube neutrinos and blazars, the most energetic particle accelerators known in the Universe.
N-body simulations for parametrized modified gravity
Authors: Hassani Farbod , Lombriser Lucas 
Published: July 2020

ABSTRACT
We present MG-evolution, an N-body code simulating the cosmological structure formation for parametrized modifications of gravity. It is built from the combination of parametrized linear theory with a parametrization of the deeply non-linear cosmological regime extrapolated from modified spherical collapse computations that cover the range of known screening mechanisms. We test MG-evolution, which runs at the speed of conventional ΛCDM simulations, against a suit of existing exact model-specific codes, encompassing linearized and chameleon f(R) gravity as well as the normal branch of the Dvali–Gabadadz–Porrati braneworld model, hence covering both large-field value and large-derivative screening effects. We compare the non-linear power spectra produced by the parametrized and model-specific approaches over the full range of scales set by the box size and resolution of our simulations, k = (0.05 − 2.5) $h\, \mathrm{Mpc}^{-1}$, and for two redshift slices, z = 0 and z = 1. We find sub-percent to one-percent level recovery of all the power spectra generated with the model-specific codes for the full range of scales. MG-evolution can be used for generalized and accurate tests of gravity and dark energy with the increasing wealth of high-precision cosmological survey data becoming available over the next decade.
Convection and spin-up during common envelope evolution: the formation of short-period double white dwarfs
Authors: Wilson E C , Nordhaus J 
Published: July 2020

ABSTRACT
The formation channels and predicted populations of double white dwarfs (DWDs) are important because a subset will evolve to be gravitational-wave sources and/or progenitors of Type Ia supernovae. Given the observed population of short-period DWDs, we calculate the outcomes of common envelope (CE) evolution when convective effects are included. For each observed white dwarf (WD) in a DWD system, we identify all progenitor stars with an equivalent proto-WD core mass from a comprehensive suite of stellar evolution models. With the second observed WD as the companion, we calculate the conditions under which convection can accommodate the energy released as the orbit decays, including (if necessary) how much the envelope must spin-up during the CE phase. The predicted post-CE final separations closely track the observed DWD orbital parameter space, further strengthening the view that convection is a key ingredient in CE evolution.
Simplification of Ribosomes in Bacteria with Tiny Genomes
Authors: Nikolaeva Daria D , Gelfand Mikhail S , Garushyants Sofya K 
Published: July 2020

AbstractThe ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (&lt;1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine–Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
Pubertal down-regulation of Tetraspanin 8 in testicular Sertoli cells is crucial for male fertility
Authors: Pradhan Bhola Shankar , Bhattacharya Indrashis , Sarkar Rajesh , Majumdar Subeer S 
Published: July 2020

Abstract
The alarming decline in sperm count has become a global concern in the recent decades. The division and differentiation of male germ cells (Gc) into sperm are governed by Sertoli cells (Sc) upon their functional maturation during puberty. However, the roles of genes regulating pubertal maturation of Sc have not been fully determined. We have observed that Tetraspanin 8 (Tspan8) is down-regulated in Sc during puberty in rats. However, there has been no in vivo evidence for a causal link between the down-regulation of Tspan8 expression and the onset of spermatogenesis as yet. To investigate this, we generated a novel transgenic (Tg) rat, in which the natural down-regulation of Tspan8 was prevented specifically in Sc from puberty up to adulthood. Adult Tg male rats showed around 98% reduction in sperm count despite having a similar level of serum testosterone (T) as the controls. Functional maturation of Sc was impaired as indicated by elevated levels of Amh and low levels of Kitlg and Claudin11 transcripts. The integrity of the blood testis barrier was compromised due to poor expression of Gja1 and Gc apoptosis was discernible. This effect was due to a significant rise in both Mmp7 and phospho P38 MAPK in Tg rat testis. Taken together, we demonstrated that the natural down-regulation of Tspan8 in Sc during puberty is a prerequisite for establishing male fertility. This study divulges one of the aetiologies of certain forms of idiopathic male infertility where somatic cell defect, but not hormonal deficiency, is responsible for impaired spermatogenesis.
A Problematic Conflation of Justice and Equality: The Case for Equity in Music Therapy
Authors: Leonard Hakeem 
Published: July 2020

AbstractA historical basis and a therapeutic foundation are given for understanding the importance of equity when considering contexts of race in music therapy, specifically with African-American or Black clients. Those contexts are broad, including, but not limited to Black clients, Black music, diversity and inclusion, safe spaces, multiculturalism, access to music therapy education, access to services. Examples are given of the Black experience in the United States related to self-definition, self-sufficiency, growth, and resiliency. Both cultural and musical aesthetic contextualization are pointed to, and connections are drawn between the navigation of Black people through different types of oppressive systems, and the negotiation of double-bind dilemmas that try to force Black disembodiment when trying to live authentic personhood in the face of proscriptive and prescriptive forces. Despite this systemic oppression, Black people continue to show a resilience in society as well as therapeutic and health settings, which is seen more readily when therapists and professionals can center in the margins the lived experience of Black clients, decenter themselves where appropriate, and practice a critical consciousness that actively uses counterhegemonic and antiracist practices. As music therapists have begun to understand joining ethics and evidence together through the self-advocacy of some populations, we must do the same while explicitly centering equity in our work with Black clients. If music therapists truly espouse justice, then there should be a critical examination of this in the profession-- in ourselves, our work, our relationship to music, our organizations, and in our education and training.
The Prepare for Kidney Care Study: prepare for renal dialysis versus responsive management in advanced chronic kidney disease
Authors: Murphy Emma , Burns Aine , Murtagh Fliss E M , Rooshenas Leila , Caskey Fergus J 
Published: July 2020

Abstract
Shared decision making in advanced chronic kidney disease (CKD) requires unbiased information on survival and person-centred outcomes known to matter to patients: quality of life, symptom burden and support from family and healthcare professionals. To date, when deciding between dialysis and conservative care, patients have had to rely on evidence from small observational studies. Clinicians recognize that like is not being compared with like in these studies, and interpret the results differently. Furthermore, support differs considerably between renal units. What patients choose therefore depends on which renal unit they attend. To address this, a programme of work has been underway in the UK. After reports on survival and symptoms from a small number of renal units, a national, mixed-methods study—the Conservative Kidney Management Assessment of Practice Patterns Study—mapped out conservative care practices and attitudes in the UK. This led to the Prepare for Kidney Care study, a randomized controlled trial comparing preparation for dialysis versus preparation for conservative care. Although powered to detect a positivist 0.345 difference in quality-adjusted life years between the two treatments, this trial also takes a realist approach with a range of person-centred secondary outcomes and embedded qualitative research. To understand generalizability, it is nested in an observational cohort study, which is nested in a CKD registry. Challenges to recruitment and retention have been rapidly identified and addressed using an established embedded mixed methods approach—the QuinteT recruitment intervention. This review considers the background to and progress with recruitment to the trial.
A molecular signature associated with prolonged survival in glioblastoma patients treated with regorafenib
Authors: Santangelo Alessandra , Rossato Marzia , Lombardi Giuseppe , Benfatto Salvatore , Lavezzari Denise , De Salvo Gian Luca , Indraccolo Stefano , Dechecchi Maria Cristina , Prandini Paola , Gambari Roberto , Scapoli Chiara , Di Gennaro Gianfranco , Caccese Mario , Eoli Marica , Rudà Roberta , Brandes Alba Ariela , Ibrahim Toni , Rizzato Simona , Lolli Ivan , Lippi Giuseppe , Delledonne Massimo , Zagonel Vittorina , Cabrini Giulio 
Published: July 2020

Abstract

Background
Patients with glioblastoma (GBM) have a dramatically poor prognosis. The recent REGOMA trial suggested an overall survival (OS) benefit of regorafenib in recurrent GBM patients. Considering the extreme genetic heterogeneity of GBMs, we aimed to identify molecular biomarkers predictive of differential response to the drug.

Methods
Total RNA was extracted from tumor samples of patients enrolled in the REGOMA trial. Genome-wide transcriptome and micro (mi)RNA profiles were associated with patients’ OS and progression-free survival.

Results
In the first step, a set of 11 gene transcripts (HIF1A, CTSK, SLC2A1, KLHL12, CDKN1A, CA12, WDR1, CD53, CBR4, NIFK-AS1, RAB30-DT) and 10 miRNAs (miR-93-5p, miR-203a-3p, miR-17-5p, let-7c-3p, miR-101-3p, miR-3607-3p, miR-6516-3p, miR-301a-3p, miR-23b-3p, miR-222-3p) was filtered by comparing survival between regorafenib and lomustine arms. In the second step, a mini-signature of 2 gene transcripts (HIF1A, CDKN1A) and 3 miRNAs (miR-3607-3p, miR-301a-3p, miR-93-5p) identified a subgroup of patients showing prolonged survival after regorafenib administration (median OS range, 10.6–20.8 mo).

Conclusions
The study provides evidence that a signature based on the expression of 5 biomarkers could help identify a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Although the presented results must be confirmed in larger replication cohorts, the study highlights potential biomarker options to help guide the clinical decision among regorafenib and other treatments in patients with relapsing GBM.