bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq
Authors: Krych Łukasz , Castro-Mejía Josué L. , Forero-Junco Laura M. , Moesby Daniel N. , Mikkelsen Morten B. , Rasmussen Morten A. , Sykulski Maciej , Nielsen Dennis S. 
Published: October 2019

AbstractDespite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.
High-fidelity endonuclease variant HypaCas9 facilitates accurate allele-specific gene modification in mouse zygotes
Authors: Ikeda Arisa , Fujii Wataru , Sugiura Koji , Naito Kunihiko 
Published: October 2019

AbstractCRISPR/Cas9 has been widely used for the efficient generation of genetically modified animals; however, this system could have unexpected off-target effects. In the present study, we confirmed the validity of a high-fidelity Cas9 variant, HypaCas9, for accurate genome editing in mouse zygotes. HypaCas9 efficiently modified the target locus while minimizing off-target effects even in a single-nucleotide mismatched sequence. Furthermore, by applying HypaCas9 to the discrimination of SNP in hybrid strain-derived zygotes, we accomplished allele-specific gene modifications and successfully generated mice with a monoallelic mutation in an essential gene. These results suggest that the improved accuracy of HypaCas9 facilitates the generation of genetically modified animals.
The Effect of Vocabulary Intervention on Text Comprehension: Who Benefits?
Authors: Duff Dawna 
Published: October 2019

Purpose
Vocabulary intervention can improve comprehension of texts containing taught words, but it is unclear if all middle school readers get this benefit. This study tests 2 hypotheses about variables that predict response to vocabulary treatment on text comprehension: gains in vocabulary knowledge due to treatment and pretreatment reading comprehension scores.

Method

Students in Grade 6 (
N
= 23) completed a 5-session intervention based on robust vocabulary instruction (RVI). Knowledge of the semantics of taught words was measured pre- and posttreatment. Participants then read 2 matched texts, 1 containing taught words (treated) and 1 not (untreated). Treated texts and taught word lists were counterbalanced across participants. The difference between text comprehension scores in treated and untreated conditions was taken as a measure of the effect of RVI on text comprehension.

Results

RVI resulted in significant gains in knowledge of taught words (

d
RM

= 2.26) and text comprehension (

d
RM

= 0.31). The extent of gains in vocabulary knowledge after vocabulary treatment did not predict the effect of RVI on comprehension of texts. However, untreated reading comprehension scores moderated the effect of the vocabulary treatment on text comprehension: Lower reading comprehension was associated with greater gains in text comprehension. Readers with comprehension scores below the mean experienced large gains in comprehension, but those with average/above average reading comprehension scores did not.

Conclusion
Vocabulary instruction had a larger effect on text comprehension for readers in Grade 6 who had lower untreated reading comprehension scores. In contrast, the amount that children learned about taught vocabulary did not predict the effect of vocabulary instruction on text comprehension. This has implications for the identification of 6th-grade students who would benefit from classroom instruction or clinical intervention targeting vocabulary knowledge.
Spoken Word Learning Differences Among Children With Dyslexia, Concomitant Dyslexia and Developmental Language Disorder, and Typical Development
Authors: Alt Mary , Gray Shelley , Hogan Tiffany P. , Schlesinger Nora , Cowan Nelson 
Published: October 2019

Purpose
The purpose of our study was to test the hypotheses (a) that children with dyslexia have spoken word learning deficits primarily related to phonology and (b) that children with dyslexia and concomitant developmental language disorder (DLD) have word learning deficits related to both phonology and semantic processing when compared to peers with typical development (TD).

Method

Second-graders with dyslexia (
n
= 82), concomitant dyslexia and DLD (dyslexia + DLD;
n
= 40), and TD (
n
= 167) learned names and semantic features for cartoon monsters in 5 carefully controlled word learning tasks that varied phonological and semantic demands. The computer-based tasks were played in 6 different word learning games. We analyzed results using Bayesian statistics.

Results
In general, the dyslexia + DLD group showed lower accuracy on tasks compared to the dyslexia and TD groups. As predicted, word learning tasks that taxed phonology revealed deficits in the dyslexia group, although there were some exceptions related to visual complexity. Word learning deficits in the dyslexia + DLD group were present in tasks that taxed phonology, semantic processing, or both.

Conclusions
The dyslexia + DLD group demonstrated word learning deficits across the range of word learning tasks that tapped phonology and semantic processing, whereas the dyslexia group primarily struggled with the phonological aspects of word learning.

Supplemental Material

https://doi.org/10.23641/asha.9807929
Erhöhte NF-κB- und iNOS-Expression in Keratozyten von Keratokonuspatienten – Hinweise auf eine entzündliche Komponente?
Authors: Stachon Tanja , Latta Lorenz , Kolev Krasimir , Seitz Berthold , Langenbucher Achim , Szentmáry Nóra 
Published: October 2019

ZusammenfassungHintergrund In den letzten Jahren mehren sich Hinweise auf eine entzündliche Komponente beim Keratokonus (KC). Ein Schlüsselgen bei entzündlichen Prozessen ist der Nuclear Factor Kappa B (NF-κB). NF-κB ist ein Transkriptionsfaktor, der unter anderem das Enzym Nitric Oxide Synthase (NOS), das mit dem konkurrierenden Enzym Arginase (Arg) bei entzündlichen Prozessen involviert ist, aktiviert. Ziel dieser Studie war es, die Isotypen von NOS und Arginase zu analysieren, die Expression NF-κB, NOS und Arginase sowie den regulativen Mechanismus von NOS und Arginase in Keratozyten von Keratokonuspatienten mithilfe des Inhibitors 1400W in vitro zu untersuchen.Methoden Primäre humane Keratozyten wurden durch enzymatische Behandlung mit Kollagenase A aus humanen Korneoskleralscheiben (n = 8) und von Explantaten von geplanten perforierenden Keratoplastiken (KC-Patienten) isoliert (n = 8) und in DMEM/F12-Kulturmedium, versetzt mit 5% fetalem Kälberserum, kultiviert. Die Expression von NF-κB, NOS und Arginase wurden mit quantitativer PCR (qPCR) und Westernblot-Analyse (WB) untersucht. Nitrit- und Ureakonzentrationen im Zellkulturüberstand wurden nach Zugabe des NOS-Inhibitors 1400W (0 – 40 µM) analysiert.Ergebnisse In den Keratozyten wurden ausschließlich die Isotypen iNOS (induzierbare NO-Synthase) und Arg-II nachgewiesen. Die mRNA-Expression von NF-κB und iNOS waren in KC-Keratozyten höher als in normalen Zellen (p = 0,0135 und p = 0,0001), während in der Arg-II-Expression keine Unterschiede messbar waren. Im WB war bei NF-κB eine höhere Bandenintensität messbar (p = 0,0012), bei iNOS konnten keine Unterschiede in der Bandenintensität nachgewiesen werden. Im Überstand der KC-Keratozyten wurden geringere Konzentrationen von Nitrit und Urea nach Zugabe des Inhibitors 1400W gemessen (p = ≤ 0,014), nicht jedoch bei normalen Zellen (p ≥ 0,178).Schlussfolgerung Aufgrund der erhöhten Expression von NF-κB und iNOS muss von einer inflammatorischen Komponente beim Keratokonus ausgegangen werden. Die unterschiedliche Regulation der KC-Keratozyten durch den iNOS-Inhibitor 1400W legt eine veränderte metabolische Aktivität nahe, die durch entzündliche Prozesse hervorgerufen werden kann.
Relationship between Duration of Infant Exposure to a Moderate-to-Large Patent Ductus Arteriosus Shunt and the Risk of Developing Bronchopulmonary Dysplasia or Death Before 36 Weeks
Authors: Clyman Ronald I. , Hills Nancy K. , Liebowitz Melissa , Johng Sandy 
Published: October 2019

Abstract
Objective This study was aimed to examine the relationship between duration of infant exposure to a moderate-to-large patent ductus arteriosus (PDA) shunt and the risk of developing bronchopulmonary dysplasia (BPD) or death before 36 weeks (BPD/death).
Study Design Infants <28 weeks' gestation who survived ≥7 days (n = 423) had echocardiograms performed on day 7 and at planned intervals.
Results In multivariable regression models, BPD/death did not appear to be increased until infants had been exposed to a moderate-to-large PDA for at least 7–13 days: OR (95%CI) (referent = closed or small PDA): moderate-to-large PDA exposure for <7 days: 0.38 (range, 0.10–1.46); for 7 to 13 days = 2.12 (range, 1.04–4.32); for ≥14 days = 3.86 (range, 2.15–6.96). Once the threshold of 7 to 13 days had been reached, additional exposure (≥14 days) did not significantly add to the increased incidence of BPD/death: (referent exposure = 7–13 days) exposure for 14 to 27 days = 1.34 (range, 0.52–3.45); for 28 to 48 days = 2.34 (range, 0.88–6.19); for ≥49 days = 1.80 (range. 0.59–5.47). A similar relationship was found for the outcome of BPD-alone.
Conclusion Infants < 28 weeks' gestation required at least 7 to 13 days of exposure to a moderate-to-large PDA before a significant increase in the incidence of BPD/death was apparent. Once this threshold was reached additional exposure to a moderate-to-large PDA did not significantly add to the increased incidence of BPD/death.
Epidural versus PCA Pain Management after Pectus Excavatum Repair: A Multi-Institutional Prospective Randomized Trial
Authors: Sujka Joseph A. , Dekonenko Charlene , Millspaugh Daniel L. , Doyle Nichole M. , Walker Benjamin J. , Leys Charles M. , Ostlie Daniel J. , Aguayo Pablo , Fraser Jason D. , Alemayehu Hanna , Peter Shawn D. St. 
Published: October 2019

Abstract
Introduction Postoperative pain control remains the primary reason for inpatient stay after minimally invasive repair of pectus excavatum. In a previous study, our group reported that early pain control was better in patients managed with a thoracic epidural, while late pain control was better in patients managed with patient-controlled analgesia (PCA). After revising our epidural transition and modifying the PCA protocol, we conducted a multi-institutional prospective randomized trial to evaluate these two pain control strategies.
Materials and Methods Patients were randomized to epidural or PCA following minimally invasive repair of pectus excavatum with standard protocols for each arm. Primary outcome was length of stay with secondary variables including mean patient pain scores, complications, and parental satisfaction. Scores were pooled for the two groups and reported as means with standard deviation. Results were compared using t-tests and one-way analysis of variance with p-value < 0.05 determining significance.
Results Sixty-five patients were enrolled, 32 epidural and 33 PCA. Enrollment was stopped early when we developed an alternative strategy for controlling these patients' pain. There was no difference in length of stay in hours between the two arms; epidural 111.3 ± 18.5 versus PCA 111.4 ± 51.4, p = 0.98. Longer operative time was found in the epidural group. Nine patients in the epidural group (28%) required a PCA in addition to epidural for adequate pain control. Mean pain scores were lower on postoperative day 0 in the epidural group compared with the PCA groups, but were otherwise similar.
Conclusion In our prospective randomized trial, PCA is just as effective as thoracic epidural in decreasing early postoperative pain scores after minimally invasive repair of pectus excavatum.
A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface
Authors: Peluso Emily A. , Updegrove Taylor B. , Chen Jiji , Shroff Hari , Ramamurthi Kumaran S. 
Published: October 2019

Significance
The assembly of localized static structures is a culminating feature of developmental programs. Construction of the spore coat, a shell that surrounds bacterial spores, is a model for understanding how proteins localize and assemble at the correct place and time during morphogenesis. Using data derived from in vivo and in vitro single-molecule imaging, we propose a computational model in which coat assembly initiates via an interplay between 2 proteins: a protein that localizes preferentially to micron-scale convex membranes (the surface of the developing spore) and a recruited structural protein that polymerizes to hold the first protein in place. This ratchet model therefore describes how a static structure can be built specifically atop the 2-dimensional surface of a developing organelle.
Traversable Lorentzian wormholes in higher dimensional theories of gravity
Authors: Baruah Anshuman , Deshamukhya Atri 
Published: October 2019

Abstract
Wormhole solutions in classical general relativity are unstable and hence non traversable. Morris and Thorne discovered a traversable wormhole solution that required the energy momentum tensor of matter sources to violate various energy conditions and are out of the purview of the standard model of particle physics. The search for traversable wormhole solutions in modified theories of gravity has been of significant interest in the decades after Morris and Thorne first published their results as such violations may be avoided in such theories. This work comprehensively reviews traversable wormhole solutions in higher dimensional extensions of general relativity that satisfy the various energy conditions with an in depth look at the matter sources and the various constraints on the parameters of the theories to make the energy momentum of the matter sources respect the energy conditions.
“The Myth Is Dead! Give Us Our History!” Reassessing Black Labor in African HistoryThe Moon Is Dead! Give Us Our Money! The Cultural Origins of an African Work Ethic, Natal, South Africa, 1843–1900, by Keletso E. Atkins
Authors: Tallie T.J. 
Published: October 2019

Abstract
Keletso Atkins’s 1993 book The Moon Is Dead! Give Us Our Money! The Cultural Origins of an African Work Ethic, Natal, South Africa, 1843–1900, remains as prescient now as it was a quarter-century ago. Atkins’s insistence on a methodology that foregrounded African labor regimes as logically consistent, rational, and deserving of full consideration within a proto-capitalist colonial market has had a significant impact in Southern African historical scholarship, and these calls have been taken up with earnest by subsequent scholars. Perhaps most important, however, has been her self-aware approach as a black scholar writing to and for members of the diaspora, an academic achievement rarely repeated in her subfield.
Differences in PD-L1–Expressing Macrophages and Immune Microenvironment in Testicular Germ Cell Tumors
Authors: Sadigh Sam , Farahani Sahar J , Shah Abhishek , Vaughn David , Lal Priti 
Published: October 2019

AbstractObjectivesTo characterize the tumor microenvironment of testicular germ cell tumors (GCTs) using immunohistochemical markers.MethodsSeventy-seven orchiectomies, including 36 nonmetastatic (NM) seminomas, 15 metastatic (M) seminomas, 13 nonmetastatic nonseminomatous germ cell tumors (NSGCTs), and 13 metastatic NSGCTs, were studied with PD-1, PD-L1, FOXP3, CD68, CD163, and mismatch repair (MMR) immunohistochemistry. FOXP3+ and PD-1+ tumor-infiltrating lymphocytes (TILs) and tumor-associated macrophages (TAMs) expressing CD68 and CD163 were enumerated. PDL-1 expression was evaluated on tumor cells and macrophages.ResultsGCTs primarily express PD-L1 on TAMs, except choriocarcinoma, where true tumor cell positivity was noted. Seminomas reveal increased intratumoral PD-L1+ TAMs compared with NSGCTs (P &lt; .05). Activated TILs are increased in NM-seminomas compared with M-seminomas (P &lt; .05). All GCTs retained MMR expression.ConclusionsRobust PD-L1+ TAMs are significantly expanded in seminomas compared with NSGCTs. Among all GCTs, only choriocarcinoma cells reveal true positivity for PD-L1. These findings expand the realm of potentially targeted treatments for GCTs.
YouTube for Cosmetic Plastic Surgery: An Effective Patient Resource?
Authors: Ward Brittany , Ayyala Haripriya S , Zhang Kathy , Manuskhani Priya A , Paskhover Boris , Lee Edward S 
Published: October 2019

Abstract

Background
YouTube is increasingly being utilized as a major educational resource by patients. It is important for plastic surgeons to understand the quality and characteristics of videos that patients are likely to view about procedures of interest.

Objectives
The aim of this study was to evaluate the quality of the videos that patients are most likely to encounter when searching YouTube for the most common cosmetic plastic surgery procedures.

Methods
Based on Google Trends data, the most searched medical and colloquial terms were identified for common cosmetic surgery procedures: “abdominoplasty,” “tummy tuck,” “breast augmentation,” “boob job,” “liposuction,” “lipo,” “mastopexy,” “breast lift,” “reduction mammoplasty,” and “breast reduction.” On YouTube, videos were searched by relevance (default) and view count; the top 10 results were collected in each group and rated according to the DISCERN criteria. Each video was assigned an overall and bias DISCERN score (DS). A score of 1 indicates high bias and low overall quality and a score of 5 indicates the opposite.

Results
In total, 143 unique videos were identified, which resulted in a mean bias DS of 2.29 and mean overall DS of 2.44. Seventy-two videos included US board-certified plastic surgeons and 58 were classified as patient experience. Videos had 667,373,209 total views and were an average of 4.27 years old. Videos including US board-certified plastic surgeons were of significantly higher quality and showed lower bias than videos without these practitioners (P &lt; 0.05).

Conclusions
Overall, YouTube videos showed high bias and low quality. Plastic surgeons should be aware of this popular resource and counsel patients about the bias that is often present. Plastic surgeons and academic plastic surgery organizations should strive to upload high-quality, unbiased videos to provide patients with a more appropriate resource.
Emotional Interference in Early Adolescence: Positive Reinforcement Modulates the Behavioral and Neural Effects of Negative Emotional Distracters
Authors: Jones Neil P , Schlund Michael , Kerestes Rebecca , Ladouceur Cecile D 
Published: October 2019

AbstractLimited research has examined functioning within fronto-limbic systems subserving the resistance to emotional interference in adolescence despite evidence indicating that alterations in these systems are implicated in the developmental trajectories of affective disorders. This study examined the functioning of fronto-limbic systems subserving emotional interference in early adolescence and whether positive reinforcement could modulate these systems to promote resistance to emotional distraction. Fifty healthy early adolescents (10–13 years old) completed an emotional delayed working memory (WM) paradigm in which no distractors (fixation crosshair) and emotional distracters (neutral and negative images) were presented with and without positive reinforcement for correct responses. WM accuracy decreased with negative distracters relative to neutral distracters and no distracters, and activation increased in amygdala and prefrontal cortical (PFC) regions (ventrolateral, dorsomedial, ventromedial, and subgenual anterior cingulate) with negative distracters compared with those with no distracters. Reinforcement improved performance and reduced activation in the amygdala, dorsomedial PFC, and ventrolateral PFC. Decreases in amygdala activation to negative distracters due to reinforcement mediated observed decreases in reaction times. These findings demonstrate that healthy adolescents recruit similar fronto-limbic systems subserving emotional interference as adults and that positive reinforcement can modulate fronto-limbic systems to promote resistance to emotional distraction.
Behavioral Pharmacology of Novel Kappa Opioid Receptor Antagonists in Rats
Authors: Page Sarah , Mavrikaki Maria M , Lintz Tania , Puttick Daniel , Roberts Edward , Rosen Hugh , Carroll F Ivy , Carlezon William A , Chartoff Elena H 
Published: October 2019

AbstractBackgroundNew treatments for stress-related disorders including depression, anxiety, and substance use disorder are greatly needed. Kappa opioid receptors are expressed in the central nervous system, including areas implicated in analgesia and affective state. Although kappa opioid receptor agonists share the antinociceptive effects of mu opioid receptor agonists, they also tend to produce negative affective states. In contrast, selective kappa opioid receptor antagonists have antidepressant- and anxiolytic-like effects, stimulating interest in their therapeutic potential. The prototypical kappa opioid receptor antagonists (e.g., norBNI, JDTic) have an exceptionally long duration of action that complicates their use in humans, particularly in tests to establish safety. This study was designed to test dose- and time-course effects of novel kappa opioid receptor antagonists with the goal of identifying short-acting lead compounds for future medication development.MethodsWe screened 2 novel, highly selective kappa opioid receptor antagonists (CYM-52220 and CYM-52288) with oral efficacy in the warm water tail flick assay in rats to determine initial dose and time course effects. For comparison, we tested existing kappa opioid receptor antagonists JDTic and LY-2456302 (also known as CERC-501 or JNJ-67953964).ResultsIn the tail flick assay, the rank order of duration of action for the antagonists was LY-2456302 < CYM-52288 < CYM-52220 << JDTic. Furthermore, LY-2456302 blocked the depressive (anhedonia-producing) effects of the kappa opioid receptor agonist U50,488 in the intracranial self-stimulation paradigm, albeit at a higher dose than that needed for analgesic blockade in the tail flick assay.ConclusionsThese results suggest that structurally diverse kappa opioid receptor antagonists can have short-acting effects and that LY-2456302 reduces anhedonia as measured in the intracranial self-stimulation test.