bluuebunny/crossref_metadata_2025 huggingface dataset:
Early Adolescent Binge Drinking Increases Risk of Psychopathology in Post-9/11 Veterans and Mild Traumatic Brain Injury Exacerbates Symptom Severity
Authors: Fortier Catherine B , Whitworth James W , Fonda Jennifer R , Currao Alyssa , Beck Brigitta M , Levin Laura , Esterman Michael , Milberg William P , McGlinchey Regina E
Published: July 2020

Aims

To demonstrate that early adolescent binge drinking (BD) increases the risk for and/or severity of psychopathology in post-9/11 Veterans and determine if mild traumatic brain injury (mTBI) modifies risk.

Methods

Post-9/11 Veterans (n = 375) were classified into two groups: 57 Veterans with a history of early adolescent BD (E-BD; age of onset <15) and 318 who did not BD until age 15 or older (late-BD or L-BD; age of onset ≥15). History of military mTBI and mental health disorders were also assessed following military service.

Results

Logistic regression and analysis of variance (ANOVA) analyses revealed that the E-BD’s had significantly higher prevalence of alcohol use disorders (AUDs) and more severe symptoms of AUD, substance use disorder (SUD), depression and stress. Two-way ANOVAs showed that history of military mTBI was differentially associated with posttraumatic stress disorder (PTSD) incidence and severity among Veterans who had engaged in early adolescent BD. Specifically, Veterans with a history of both early adolescent BD and military mTBI were at greater risk for a PTSD diagnosis and had more severe symptoms of PTSD than those with only a history of adolescent BD. The greater PTSD symptom severity in the comorbid group was driven by hyperarousal symptoms.

Conclusions

A history of BD during early adolescence is prevalent among Veterans and is related to higher risk for AUD and more severe AUD, SUD, mood and stress symptoms later in life. Veterans with early BD and military mTBI showed greater incidence and severity of PTSD, indicating that mTBI, a common comorbidity among post-9/11 Veterans, exacerbates risk.
Evaluation of Methods for Sampling of Staphylococcus aureus and Other Staphylococcus Species from Indoor Surfaces
Authors: Madsen Anne Mette , Phan Hoang U T , Laursen Mathias , White John K , Uhrbrand Katrine
Published: July 2020

Objectives

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing public and occupational health concern. As transmission of MRSA can occur via contact with fomites, it is crucial to have sensitive methods for sampling of bacteria. The overall aim of this study was to obtain knowledge about methods and strategies for quantitative sampling Staphylococcus species on surfaces.

Methods

The study was designed as a comparative sampling experiment with different samplers [dipslide (two agar types), swabs (three brands, used wet and dry, and elution from swabs or plate diluted)] on smooth stainless steel surfaces spiked with MRSA and methicillin-sensitive S. aureus (MSSA). Furthermore, bacteria sampled from indoor surfaces with frequent or infrequent contact with hands were quantified and identified using matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS).

Results

Pre-moistened swabs in combination with dilution plating and dipslides were more sensitive than dry swabs. For recovery of MRSA and MSSA from surfaces with eSwabs, at least 0.3–100 CFU MRSA cm−2 and 5.3–8.6 CFU MSSA cm−2 should be present. The sensitivities of pre-moistened eSwabs were approximately 10-fold higher than those of dipslides and pre-moistened viscose and cotton swabs. The variation in concentrations of Staphylococcus species in replicate sampling of adjacent squares on indoor surfaces was higher for surfaces frequently touched by hands than for surfaces infrequently touched. In total 16 different Staphylococcus species were identified, and S. aureus was found only in 2 of 66 surface samples. A considerable overlap was found between species in replicate sampling within an environment and between the air and surfaces within an environment.

Conclusions

Pre-moistened eSwabs in combination with dilution plating were found to be the best method for surface sampling of MSSA and MRSA. The method can be used for assessing the risk of exposure and transmission of MRSA from environmental surfaces. To obtain a reliable measure of concentrations and the presence of Staphylococccus species a higher number of samples should be taken from surfaces with hand contact than from surfaces dominated by sedimented bacteria.
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events
Authors: Zhang Shihua , He Xiaolong , Zhang Rui , Deng Wensheng
Published: July 2020

Mounting evidence has shown the involvement of long non-coding RNAs (lncRNAs) during various cancer metastatic events (abbreviated as CMEs, e.g. cancer cell invasion, intravasation, extravasation, proliferation, etc.) that may cooperatively facilitate malignant tumor spread and cause massive patient deaths. The study of lncRNA-CME associations might help understand lncRNA functions in metastasis and present reliable biomarkers for early dissemination detection and optimized treatment. Therefore, we developed a database named ‘lncR2metasta’ by manually compiling experimentally supported lncRNAs during various CMEs from existing studies. LncR2metasta documents 1238 associations between 304 lncRNAs and 39 CMEs across 54 human cancer subtypes. Each entry of lncR2metasta contains detailed information on a lncRNA-CME association, including lncRNA symbol, a specific CME, brief description of the association, lncRNA category, lncRNA Entrez or Ensembl ID, lncRNA genomic location and strand, lncRNA experiment, lncRNA expression pattern, detection method, target gene (or pathway) of lncRNA, lncRNA regulatory role on a CME, cancer name and the literature reference. An easy-to-use web interface was deployed in lncR2metasta for its users to easily browse, search and download as well as to submit novel lncRNA-CME associations. LncR2metasta will be a useful resource in cancer research community. It is freely available at http://lncR2metasta.wchoda.com.
Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers
Authors: Zhang Peng , Liu Mingyue , Cui Ya , Zheng Pan , Liu Yang
Published: July 2020

Based on clinical outcomes in colorectal cancer, high microsatellite instability (MSI-H) has recently been approved by the Food and Drug Administration (FDA) as a genetic test to select patients for immunotherapy targeting PD-1 and/or CTLA-4 without limitation to cancer type. However, it is unclear whether the MSI-H would broadly alter the tumor microenvironment to confer the therapeutic response of different cancer types to immunotherapy. To fill in this gap, we performed an in silico analysis of tumor immunity among different MSI statuses in five cancer types. We found that consistent with clinical responses to immunotherapy, MSI-H and non-MSI-H samples from colorectal cancer (COAD-READ) exhibited distinct infiltration levels and immune phenotypes. Surprisingly, the immunological difference between MSI-H and non-MSI-H samples was diminished in stomach adenocarcinoma and esophageal carcinoma (STAD-ESCA) and completely disappeared in uterine corpus endometrial carcinoma (UCEC). Regardless of cancer types, the abundance of tumor-infiltrating immune cells, rather than MSI status, strongly associated with the clinical outcome. Since preexisting antitumor immune response in the tumor (hot cancer) is accepted as a prerequisite to the therapeutic response to anti-PD-1/CTLA-4 immunotherapy, our data demonstrate that the impact of MSI varied on immune contexture will lead to the further evaluation of predictive immunotherapy responsiveness based on the universal biomarker of MSI status.
An Analysis of US State Regulated Weed Lists: A Discordance between Biology and Policy
Authors: Lakoba Vasiliy T , Brooks Rachel K , Haak David C , Barney Jacob N
Published: July 2020

Weedy and invasive plants threaten our food supply, native biodiversity, and the structure and function of ecosystems. The number and impact of these damaging plants are expected to continue to grow with ongoing global change. Some of the most common policy tools to help mitigate this threat are regulatory weed lists, which limit the importation and movement of listed plant species, but there has never been a comprehensive analysis of plants regulated in the United States. We analyzed US state regulatory lists (e.g., noxious, invasive, prohibited) to evaluate their composition, patterns of listing, congruities with weed distributions, and limitations. In total, 46 states maintain regulatory weed lists that include 3210 total listings of 1249 unique species; 48% of them are introduced, 40% are native, and 12% are not yet found in the United States. Overall, the listed species are not a good reflection of the weeds in each state, and listing appears largely reactive, regulating species after they become widespread. We highlight patterns and incongruities among lists and discuss their implications, especially the large number of regulated species native to the United States.
Grief As It Is: Genre and Narrative Withholding in the Miserable Memoir
Authors: Schaeffer Tesla
Published: July 2020

One of the consequences of the so-called “memoir boom” of the 1990s and early 2000s is that it both reflected and generated an enormous hunger for memoirs of grief and suffering; these memoirs combine to provide that increasingly codified genre of storytelling (what the Bookseller magazine and industry jargon term “misery lit”) with fixed conventions. Here, I look at two memoirs, Helene Cooper’s The House at Sugar Beach (2009) and Joan Didion’s The Year of Magical Thinking (2007), in order to trace writerly strategies of resistance against the modes of interpretation that the genre expectations of the grief memoir create. I analyze the moves that the writers make in order to honor the stories they tell despite the pressures that attend generic discourses of suffering, including where those discourses are moored to racial and gender associations.
Diversity of Gall-Inducing Insects Associated With a Widely Distributed Tropical Tree Species: Testing the Environmental Stress Hypothesis
Authors: Fagundes Marcílio , Cuevas-Reyes Pablo , Ramos Leite Letícia F , Borges Magno Augusto Zazá , De Araújo Walter Santos , Fernandes G Wilson , Siqueira Walisson Kenedy
Published: July 2020

Abiotic factors can affect plant performance and cause stress, which in turn affects plant–herbivore interactions. The Environmental Stress Hypothesis (ESH) predicts that gall-inducing insect diversity will be greater on host plants that grow in stressful habitats. We tested this hypothesis, considering both historical and ecological scales, using the plant Copaifera langsdorffii Desf. (Fabaceae) as a model because it has a wide geographic distribution and is a super-host of gall-inducing insects. According to the ESH, we predicted that 1) on a historical scale, the diversity of gall-inducing insects will be higher in habitats with greater environmental stress and 2) on an ecological scale, gall-inducing insect diversity will be greater on plants that possess greater levels of foliar sclerophylly. We sampled gall-inducing insects on plants of C. langsdorffii in five sites with different levels of water and soil nutrient availability and separated from each other by a distance of up to 470 km. The composition, richness, and abundance of gall-inducing insects varied among study sites. Plants located in more stressful habitats had higher levels of foliar sclerophylly; but richness and abundance of gall-inducing insects were not affected by host plant sclerophylly. Habitat stress was a good predictor of gall-inducing insect diversity on a regional scale, thus corroborating the first prediction of the ESH. No relationship was found between plant sclerophylly and gall-inducing insect diversity within habitats. Therefore, on a local scale, we did not find support for our second prediction related to the ESH.
Role of levosimendan in weaning children requiring veno-arterial extracorporeal membrane oxygenation after cardiac surgery
Authors: Pan Kevin C , Shankar Sai , Millar Johnny , Chiletti Roberto , Butt Warwick , d’Udekem Yves , Namachivayam Siva P
Published: July 2020

OBJECTIVES

Levosimendan use is associated with more successful decannulation from veno-arterial extracorporeal membrane oxygenation (VA ECMO) in adults. We sought to determine the role of levosimendan in children who required VA ECMO after cardiac surgery.

METHODS

This observational study compares the outcomes of children who required VA ECMO after cardiac surgery and received levosimendan for weaning with those who did not receive the drug. A doubly robust estimation methodology (inverse probability of treatment weighting with regression adjustment) was used to balance study covariates (age, weight, sex, lactate pre-ECMO, vasoactive-inotropic score pre-ECMO, ECMO indication, ECMO modality, Risk Adjustment for Congenital Heart Surgery-1 category), and the final model was further adjusted for duration of ECMO.

RESULTS

Between January 2012 and December 2018, 118 eligible children received 145 ECMO runs [failed weaning from cardiopulmonary bypass, 67/145 (46%); low cardiac output state, 30/145 (21%); extracorporeal cardiopulmonary resuscitation, 47/145 (32%); other reasons in 1]. Levosimendan was administered before decannulation in 54/145 (37%) runs. The median time to start levosimendan after ECMO cannulation was 39 h (interquartile range, 14–83 h). The unadjusted rates of weaning failure in the levosimendan vs control group were 7% (4/54) vs 19% (17/91). In the controlled analysis, levosimendan was associated with decreased risk of weaning failure [adjusted relative risk (95% confidence interval), 0.20 (0.07–0.57)] and decreased risk of in-hospital mortality [adjusted relative risk (95% confidence interval), 0.45 (0.26–0.76)].

CONCLUSIONS

Levosimendan administration in children requiring VA ECMO after cardiac surgery was associated with decreased risk of weaning failure and decreased in-hospital mortality.
The agricultural impacts of armed conflicts: the case of Fulani militia
Authors: George Justin , Adelaja Adesoji , Awokuse Titus O
Published: July 2020

Fulani ethnic militia (FEM) violence has increased significantly in recent years, making it one of the most lethal groups in the world. However, empirical evidence on the impacts of FEM on agriculture is scarce. We investigate the agricultural impacts of such violence in the case of Nigeria using a nationally representative panel dataset and armed conflict data. We find that increased FEM violence reduces agricultural output, outputs of specific staple crops and area harvested. FEM violence also reduces farmers’ cattle holdings by increasing cattle thefts and losses and reducing purchased cattle. The agricultural development implications of the FEM cannot be ignored.
Association of age at first drink and first alcohol intoxication as predictors of mortality: a birth cohort study
Authors: Levola Jonna , Rose Richard J , Mustonen Antti , Sarala Marian , Miettunen Jouko , Koskela Jari , Niemelä Anni-Emilia , Niemelä Solja
Published: July 2020

Background

More information on the health-related repercussions of age at onset of adolescent drinking is needed. The aim of this study was to examine the associations between self-reported age at first drink and age at first alcohol intoxication with the risk of death by age 30.

Methods

The sample (n = 6564; 49.1% males) included all participants of the Northern Finland Birth Cohort Study 1986 (NFBC1986) for whom the two measures of adolescent drinking were available. Self-reported age at onset of first drink and first alcohol intoxication were analyzed along with background variables and data regarding subsequent psychiatric diagnoses. Adolescents were dichotomized into those reporting age at first drink and age at first intoxication before or after age 14. Cox regression was used to calculate hazard ratios (HRs) with 95% confidence interval (95% CI) for death by age 30.

Results

By the age of 30, 0.7% (n = 47) of all 6564 participants were deceased. In the multivariable models, male gender and a history of illicit substance use in adolescence were associated with both all-cause mortality and mortality due to accidents or suicide. After controlling for confounding variables, age at first alcohol intoxication was associated with all-cause mortality (HR 2.33; 95% CI 1.04–5.20) as well as death due to accidents or suicide (HR 2.99; 95% CI 1.11–8.05).

Conclusions

Earlier age at first intoxication carries long-term repercussions with respect to premature loss of life. Efforts should be made targeting the prolongation of initiating binge drinking in adolescence to diminish this mortality risk.
Does partnership diversity in intersectoral policymaking matter for health promoting intervention packages’ composition? A multiple-case study in the Netherlands
Authors: Grêaux K M , de Vries N K , Bessems K M H H , Harting J , van Assema P
Published: July 2020

Intersectoral policymaking to improve public health includes integrated health promotion (HP) intervention packages that address a variety of health behavior determinants. The involvement of different partners is assumed to be necessary to implement such integrated packages. We examined how partnership diversity was associated with the composition of intervention packages implemented in Dutch municipalities. In a longitudinal multiple-case study (2012–14), we collected questionnaire data among 31 project leaders and 152 intervention implementers in 31 (alliances of) municipalities. Package composition was assessed in terms of intervention strategies, implementation settings and targeted behavioral determinants. Partnership diversity during the adoption and implementation phases was assessed in terms of the actors and sectors, as well as private partners and citizens involved. The association between partnership diversity and package composition was examined using crosstabs. Almost all packages integrated multiple strategies, but mostly education, facilitation and case finding, in multiple, but mostly health and public settings, such as schools. The packages targeted diverse behavioral determinants, although mainly personal and social environmental factors. A variety of partners from multiple sectors was involved, during both adoption and implementation of the packages. However, partners from the health, welfare and education sectors were mostly involved. More partnership diversity, especially during implementation, was associated with more integrated intervention packages. In intersectoral policymaking, investment in diversely composed partnerships seems worthwhile for implementing integrated intervention packages. However, investments in other conditions, like framing health issues and network management, are also needed to make environmental determinants of health behavior the object of HP.
Genetics of early growth traits
Authors: Cousminer Diana L , Freathy Rachel M
Published: July 2020

In recent years, genome-wide association studies have shed light on the genetics of early growth and its links with later-life health outcomes. Large-scale datasets and meta-analyses, combined with recently developed analytical methods, have enabled dissection of the maternal and fetal genetic contributions to variation in birth weight. Additionally, longitudinal approaches have shown differences between the genetic contributions to infant, childhood and adult adiposity. In contrast, studies of adult height loci have shown strong associations with early body length and childhood height. Early growth-associated loci provide useful tools for causal analyses: Mendelian randomization (MR) studies have provided evidence that early BMI and height are causally related to a number of adult health outcomes. We advise caution in the design and interpretation of MR studies of birth weight investigating effects of fetal growth on later-life cardiometabolic disease because birth weight is only a crude indicator of fetal growth, and the choice of genetic instrument (maternal or fetal) will greatly influence the interpretation of the results. Most genetic studies of early growth have to date centered on European-ancestry participants and outcomes measured at a single time-point, so key priorities for future studies of early growth genetics are aggregation of large samples of diverse ancestries and longitudinal studies of growth trajectories.
Direct-Acting Antivirals and Organ Transplantation: Is There Anything We Can’t Do?
Authors: Kappus Matthew R , Wolfe Cameron R , Muir Andrew J
Published: July 2020

The opioid epidemic has resulted in an increase in organ donors with hepatitis C virus (HCV) infection in the United States. With the development of direct-acting antiviral regimens that offer high sustained virologic response rates even in the setting of immunosuppression after transplantation, these HCV-viremic organs are now being offered to transplant candidates with or without preexisting HCV infection. Strategies for HCV treatment with HCV-viremic organs have included delayed and preemptive approaches. This review will discuss key studies in the different solid organ transplants, recent reports of adverse events, and ethical and regulatory considerations. The efficacy of current HCV therapies has created this important opportunity to improve survival for patients with end-organ failure through greater access to organ transplantation and decreased waitlist mortality rate.
Rotavirus Disease and Genotype Diversity in Older Children and Adults in Australia
Authors: Donato Celeste M , Roczo-Farkas Susie , Kirkwood Carl D , Barnes Graeme L , Bines Julie E
Published: July 2020

Background

Rotavirus is a major cause of gastroenteritis in children <5 years of age. The disease burden in older children, adults, and the elderly is underappreciated. This study describes rotavirus disease and genotypic diversity in the Australian population comprising children ≥5 years of age and adults.

Methods

Rotavirus positive fecal samples were collected from laboratories Australia-wide participating in the Australian Rotavirus Surveillance Program between 2010 and 2018. Rotavirus samples were genotyped using a heminested multiplex reverse-transcription polymerase chain reaction. Notification data from the National Notifiable Diseases Surveillance System were also analyzed.

Results

Rotavirus disease was highest in children aged 5–9 years and adults ≥85 years. G2P[4] was the dominant genotype in the population ≥5 years of age. Genotype distribution fluctuated annually and genotypic diversity varied among different age groups. Geographical differences in genotype distribution were observed based on the rotavirus vaccine administered to infants <1 year of age.

Conclusions

This study revealed a substantial burden of rotavirus disease in the population ≥5 years of age, particularly in children 5–9 years and the elderly. This study highlights the continued need for rotavirus surveillance across the population, despite the implementation of efficacious vaccines.
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

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

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

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

Population 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 (< 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

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.
The Bryennios List and its Origin
Authors: Stevens Luke J
Published: July 2020

The Bryennios List, often regarded as the earliest extant Old Testament canon, is here shown instead to originate from an excerpt of Epiphanius’s Weights and Measures in a medieval florilegium, the Doctrina patrum, and thus to have no independent value. Implications are briefly considered.
Eccentric grazing envelope evolution towards Type IIb supernova progenitors
Authors: Shishkin Dmitry , Soker Noam
Published: July 2020

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

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

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

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

The 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 (<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

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

A 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

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

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.