bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of probiotics in infantile colic: A rapid review
Authors: Karkhaneh Mohammad , Fraser Lexa , Jou Hsing , Vohra Sunita 
Published: April 2019

AbstractBackgroundInfantile colic (IC) is a troubling condition with limited treatment options for young infants. This rapid review aims to synthesize the evidence for probiotics in the treatment and prevention of IC in healthy term infants.MethodsWe searched in MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews for systematic reviews (SRs), and randomized control trials (RCTs) published between January 1, 2000 and July 11, 2018. Trials were included if they recruited healthy full-term infants who received probiotics for treatment or prevention of colic. The quality of evidence was assessed using GRADE criteria. As supplementary information, the safety of probiotics in infants was searched within the reviewed studies and other recent publications.ResultsWe identified four SRs and meta-analyses that included six RCTs, and found an additional three RCTs evaluating probiotics for the treatment of IC. One SR and six RCTs were identified for prevention of IC; four of the RCTs were included in the SR and two were published later. The probiotic Lactobacillus reuteri was used in the majority (five of eight) of treatment trials, and was found to significantly reduce crying in colicky breast-fed infants compared to placebo. Only two of the six prevention trials showed a significant decrease in crying time compared to placebo, although another two trials showed other benefits of probiotics, including reduced use of medications (simethicone and cimetropium bromide) and physician visits. No adverse events were identified in the included studies; other research suggests probiotics are generally safe in healthy children.ConclusionThis rapid review identified limited but favourable evidence of benefit of using probiotics for the treatment of IC in full-term breast-fed infants. While routine use of probiotics for treating or preventing IC cannot yet be recommended, it can be an option to manage IC.
Effect of Blood Flow Restriction Training on Quadriceps Muscle Strength, Morphology, Physiology, and Knee Biomechanics Before and After Anterior Cruciate Ligament Reconstruction: Protocol for a Randomized Clinical Trial
Authors: Erickson Lauren N , Lucas Kathryn C Hickey , Davis Kylie A , Jacobs Cale A , Thompson Katherine L , Hardy Peter A , Andersen Anders H , Fry Christopher S , Noehren Brian W 
Published: April 2019

Abstract

Background
Despite best practice, quadriceps strength deficits often persist for years after anterior cruciate ligament reconstruction. Blood flow restriction training (BFRT) is a possible new intervention that applies a pressurized cuff to the proximal thigh that partially occludes blood flow as the patient exercises, which enables patients to train at reduced loads. This training is believed to result in the same benefits as if the patients were training under high loads.

Objective
The objective is to evaluate the effect of BFRT on quadriceps strength and knee biomechanics and to identify the potential mechanism(s) of action of BFRT at the cellular and morphological levels of the quadriceps.

Design
This will be a randomized, double-blind, placebo-controlled clinical trial.

Setting
The study will take place at the University of Kentucky and University of Texas Medical Branch.

Participants
Sixty participants between the ages of 15 to 40 years with an ACL tear will be included.

Intervention
Participants will be randomly assigned to (1) physical therapy plus active BFRT (BFRT group) or (2) physical therapy plus placebo BFRT (standard of care group). Presurgical BFRT will involve sessions 3 times per week for 4 weeks, and postsurgical BFRT will involve sessions 3 times per week for 4 to 5 months.

Measurements
The primary outcome measure was quadriceps strength (peak quadriceps torque, rate of torque development). Secondary outcome measures included knee biomechanics (knee extensor moment, knee flexion excursion, knee flexion angle), quadriceps muscle morphology (physiological cross-sectional area, fibrosis), and quadriceps muscle physiology (muscle fiber type, muscle fiber size, muscle pennation angle, satellite cell proliferation, fibrogenic/adipogenic progenitor cells, extracellular matrix composition).

Limitations
Therapists will not be blinded.

Conclusions
The results of this study may contribute to an improved targeted treatment for the protracted quadriceps strength loss associated with anterior cruciate ligament injury and reconstruction.
On torsion-free nilpotent loops
Authors: Mostovoy Jacob , Pérez-Izquierdo José M , Shestakov Ivan P 
Published: April 2019

Abstract
We show that a torsion-free nilpotent loop (that is, a loop nilpotent with respect to the dimension filtration) has a torsion-free nilpotent left multiplication group of, at most, the same class. We also prove that a free loop is residually torsion-free nilpotent and that the same holds for any free commutative loop. Although this last result is much stronger than the usual residual nilpotence of the free loop proved by Higman, it is established, essentially, by the same method.
Exact solution to a Liouville equation with Stuart vortex distribution on the surface of a torus
Authors: Sakajo Takashi 
Published: April 2019

A steady solution of the incompressible Euler equation on a toroidal surface

T

R
,
r

of major radius
R
and minor radius
r
is provided. Its streamfunction is represented by an exact solution to the modified Liouville equation,

∇

T

R
,
r

2

ψ
=
c

e

d
ψ

+
(

8

/

d

)
κ

, where

∇

T

R
,
r

2

and
κ
denote the Laplace–Beltrami operator and the Gauss curvature of the toroidal surface respectively, and
c
,
d
are real parameters with
cd
< 0. This is a generalization of the flows with smooth vorticity distributions owing to Stuart (Stuart 1967
J. Fluid Mech.
29
, 417–440. (
doi:10.1017/S0022112067000941
)) in the plane and Crowdy (Crowdy 2004
J. Fluid Mech.
498
, 381–402. (
doi:10.1017/S0022112003007043
)) on the spherical surface. The flow consists of two point vortices at the innermost and the outermost points of the toroidal surface on the same line of a longitude, and a smooth vorticity distribution centred at their antipodal position. Since the surface of a torus has non-constant curvature and a handle structure that are different geometric features from the plane and the spherical surface, we focus on how these geometric properties of the torus affect the topological flow structures along with the change of the aspect ratio
α
=
R
/
r
. A comparison with the Stuart vortex on the flat torus is also made.
Autochthonous faecal virome transplantation (FVT) reshapes the murine microbiome after antibiotic perturbation
Authors: Draper Lorraine A. , Ryan Feargal J. , Dalmasso Marion , Casey Pat G. , McCann Angela , Velayudhan Vimalkumar , Ross R. Paul , Hill Colin 
Published: April 2019

AbstractBackgroundIt has become increasingly apparent that establishing and maintaining a complex and diverse gut microbiome is fundamental to human health. There are growing efforts to identify methods that can modulate and influence the microbiome, especially in individuals who due to disease or circumstance have experienced a disruption in their native microbiome. Faecal microbial transplantation (FMT) is one method that restores diversity to the microbiome of an individual by introducing microbes from a healthy donor. FMT introduces a complete microbiome into the recipient, including the bacteriome, archaeome, mycome and virome. In this study we investigated whether transplanting an autochthonous faecal virome consisting primarily of bacteriophages could impact a bacteriome disrupted by antibiotic treatment (FaecalViromeTransplantation;FVT).ResultsFollowing disruption of the bacteriome by penicillin and streptomycin, test mice (n=8) received a bacteria free, faecal transplant, while Control mice (n=8) received a heated and nuclease treated control. The bacteriomes (as determined via 16S rRNA sequencing) of mice that received an FVT, in which bacteriophages predominate, separated from those of the Control mice as determined by principle co-ordinate analysis (PCoA), and contained differentially abundant taxa that reshaped the bacteriome profile such that it more closely resembled that of the pre-treatment mice. Similarly, metagenomic sequencing of the virome confirmed that the bacteriophages present in the gut of treatment and Control mice differed over time in both abundance and diversity, with transplanted phages seen to colonise the FVT mice.ConclusionsAn autochthonous virome transplant impacts on the bacteriome and virome of mice following antibiotic treatment. The virome, consisting mainly of bacteriophages, reshapes the bacteriome such that it more closely resembles the pre-antibiotic state. To date, faecal transplants have largely focussed on transferring living microbes, but given that bacteriophage are inert biological entities incapable of colonising in the absence of a sensitive host they could form a viable alternative that may have fewer safety implications and that could be delivered as a robust formulation.
Copy number variant syndromes are frequent in schizophrenia: progressing towards a CNV-schizophrenia model
Authors: Sriretnakumar Venuja , Zai Clement C. , Wasim Syed , Barsanti-Innes Brianna , Kennedy James L. , So Joyce 
Published: April 2019

ABSTRACTThe genetic underpinnings of schizophrenia (SCZ) remain unclear. SCZ genetic studies thus far have only identified numerous single nucleotide polymorphisms with small effect sizes and a handful of copy number variants (CNVs). This study investigates the prevalence of well-characterized CNV syndromes and candidate CNVs within a cohort of 348 SCZ patients, and explores correlations to their phenotypic findings. There was an enrichment of syndromic CNVs in the cohort, as well as brain-related and immune pathway genes within the detected CNVs. SCZ patients with brain-related CNVs had increased CNV burden, neurodevelopmental features, and types of hallucinations. Based on these results, we propose a CNV-SCZ model wherein specific phenotypic profiles should be prioritized for CNV screening within the SCZ patient population.
Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Authors: Dayama Gargi , Priya Sambhawa , Niccum David E. , Khoruts Alexander , Blekhman Ran 
Published: April 2019

AbstractCystic Fibrosis (CF) is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in theCFTRgene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions. Advancements in medical care have lead to markedly increased longevity of patients with CF, but new complications have emerged, such as early onset of colorectal cancer (CRC). Although the pathogenesis of CRC in CF remains unclear, altered host-microbe interactions might play a critical role. Here, we characterize the changes in the gut microbiome and host gene expression in colonic mucosa of CF patients relative to healthy controls. We find that CF patients show decreased microbial diversity, decreased abundance of taxa such asButyricimonas, Sutterella,and Ruminococcaceae, and increased abundance of other taxa, such as Actinobacteria and Firmicutes. We find that 1543 genes, includingCFTR,show differential expression in the colon of CF patients compared to healthy controls. Interestingly, we find that these genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of CRC, tumor suppression, cellular dysfunction, p53 and mTOR signaling pathways. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression, and identified CRC-related genes, includingLCN2andDUOX2,for which gene expression is correlated with the abundance of CRC-associated bacteria, such as Ruminococcaceae andVeillonella. Our results provide new insight into the role of host-microbe interactions in the etiology of CRC in CF.
Early Hippocampal Sharp-Wave Ripple Deficits Predict Later Learning and Memory Impairments in an Alzheimer’s Disease Mouse Model
Authors: Jones Emily A. , Gillespie Anna K. , Yoon Seo Yeon , Frank Loren M. , Huang Yadong 
Published: April 2019

SUMMARYAlzheimer’s disease (AD) is characterized by progressive memory loss, and there is a pressing need to identify early pathophysiological alterations that predict subsequent memory impairment. Hippocampal sharp-wave ripples (SWRs) – electrophysiological signatures of memory reactivation in the hippocampus – are a compelling candidate for doing so. Mouse models of AD show reductions in both SWR abundance and associated slow gamma (SG) power during aging, but these alterations have yet to be directly linked to memory impairments. In aged apolipoprotein E4 knock in (apoE4-KI) mice – a model of the major genetic risk factor for AD – we found that reduced SWR abundance and associated CA3 SG power predicted spatial memory impairments measured 1–2 months later. Importantly, SWR-associated CA3 SG power reduction in young apoE4-KI mice also predicted spatial memory deficits measured 10 months later. These results establish features of SWRs as potential functional biomarkers of memory impairment in AD.
Controllability Governs the Balance Between Pavlovian and Instrumental Action Selection
Authors: Dorfman Hayley M. , Gershman Samuel J. 
Published: April 2019

AbstractA Pavlovian bias to approach reward-predictive cues and avoid punishment-predictive cues can conflict with instrumentally-optimal actions. While most previous work has assumed that this bias is a fixed trait, we argue that it can vary within an individual. In particular, we propose that the brain arbitrates between Pavlovian and instrumental control by inferring which is a better predictor of reward. The instrumental predictor is more flexible; it can learn values that depend on both stimuli and actions, whereas the Pavlovian predictor learns values that depend only on stimuli. The arbitration theory predicts that the Pavlovian predictor will be favored when rewards are relatively uncontrollable, because the additional flexibility of the instrumental predictor is not useful. Consistent with this hypothesis, we find that the Pavlovian approach bias is stronger under low control compared to high control contexts.
Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia
Authors: Rendeiro André F. , Krausgruber Thomas , Fortelny Nikolaus , Zhao Fangwen , Penz Thomas , Farlik Matthias , Schuster Linda C. , Nemc Amelie , Tasnády Szabolcs , Réti Marienn , Mátrai Zoltán , Alpar Donat , Bödör Csaba , Schmidl Christian , Bock Christoph 
Published: April 2019

AbstractChronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). We identified a consistent regulatory program shared across all patients, which was further validated by an independent CLL cohort. In CLL cells, this program starts with a sharp decrease of NF-κB binding, followed by reduced regulatory activity of lineage-defining transcription factors (including PAX5 and IRF4) and erosion of CLL cell identity, finally leading to the acquisition of a quiescence-like gene signature which was shared across several immune cell types. Nevertheless, we observed patient-to-patient variation in the speed of its execution, which we exploited to predict patient-specific dynamics in the response to ibrutinib based on pre-treatment samples. In aggregate, our study describes the cellular, molecular, and regulatory effects of therapeutic B cell receptor inhibition in CLL at high temporal resolution, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring.
Voltage-dependent activation of Rac1 by Nav1.5 channels promotes cell migration
Authors: Yang Ming , James Andrew D. , Suman Rakesh , Kasprowicz Richard , Nelson Michaela , O’Toole Peter J. , Brackenbury William J. 
Published: April 2019

AbstractIon channels can regulate the plasma membrane potential (Vm) and cell migration as a result of altered ion flux. However, the mechanism by which Vm regulates motility remains unclear. Here, we show that the Nav1.5 sodium channel carries persistent inward Na+ current which depolarizes the resting Vm at the timescale of minutes. This Nav1.5-dependent Vm depolarization increases Rac1 colocalization with phosphatidylserine, to which it is anchored at the leading edge of migrating cells, promoting Rac1 activation. A genetically-encoded FRET biosensor of Rac1 activation shows that depolarization-induced Rac1 activation results in acquisition of a motile phenotype. By identifying Nav1.5-mediated Vm depolarization as a regulator of Rac1 activation, we link ionic and electrical signaling at the plasma membrane to small GTPase-dependent cytoskeletal reorganization and cellular migration. We uncover a novel and unexpected mechanism for Rac1 activation, which fine tunes cell migration in response to ionic and/or electric field changes in the local microenvironment.
Patterns of urine scent mark pheromone evolution in house mice and relatives (Muridae:Mus)
Authors: Sheehan Michael J , Campbell Polly , Miller Caitlin H 
Published: April 2019

ABSTRACTScent marks are important mediators of territorial behavior and sexual selection in many species, especially among mammals. As such, the evolution of compounds used in scent marks has the potential to inform our understanding of signal evolution in relation to social and sexual selection. A major challenge in studies of chemical communication is that the link between semiochemical compounds and genetic changes is often unclear. The major urinary proteins (MUPs) of house mice are elaborated pheromone blends that provide information on sex, status and individual identity. Importantly, MUPs are a direct protein product of genes, providing a clear link between genotype and phenotype. Here we examine the evolution of urinary pheromone signals among house mice and relatives by examining the sequences and patterns of expression of MUPs in the liver, where urine excreted MUPs are produced. MUP patterns have evolved among mouse species both by gene duplication and variation in expression. Notably, the sex-specificity of pheromone expression that has previously been assumed to be male-specific varies considerably across species. Our data reveal that individual identity signals in MUPs evolved prior to 0.35 million years ago and have rapidly diversified through recombining a modest number of perceptually salient amino acid variants. Amino acid variants are much more common on the exterior of the protein where they could interact with vomeronasal receptors, suggesting that perception have played a major role in shaping MUP diversity. Collectively, these data provide new insights into the diverse processes and pressures shaping pheromone signals, and suggest new avenues for using house mice and their wild relatives to probe the evolution of signals and signal processing.
Regulation of subcellular dendritic synapse specificity by axon guidance cues
Authors: Sales Emily C. , Heckman Emily L. , Warren Timothy L. , Doe Chris Q. 
Published: April 2019

AbstractNeural circuit assembly occurs with subcellular precision, yet the mechanisms underlying this precision remain largely unknown. Subcellular synaptic specificity could be achieved by molecularly distinct subcellular domains that locally regulate synapse formation, or by axon guidance cues restricting access to one of several acceptable targets. We address these models using twoDrosophilaneurons: the dbd sensory neuron and the A08a interneuron. In wild-type larvae, dbd synapses with the A08a medial dendrite but not the A08a lateral dendrite. dbd-specific overexpression of the guidance receptors Unc-5 or Robo-2 results in lateralization of the dbd axon, which forms anatomical and functional monosynaptic connections with the A08a lateral dendrite. We conclude that axon guidance cues, not molecularly distinct dendritic arbors, are a major determinant of dbd-A08a subcellular synapse specificity.
Dental caries in human evolution: frequency of carious lesions in South African fossil hominins
Authors: Towle Ian , Irish Joel D. , De Groote Isabelle , Fernée Christianne 
Published: April 2019

AbstractCaries frequencies in South African fossil hominins were observed and compared with other hominin samples. Species studied includeParanthropus robustus,Homo naledi,Australopithecus africanus,early HomoandA. sediba. Teeth were viewed macroscopically with Micro-CT scans used to confirm lesions. Position and severity of each lesion were also noted and described. For all South African fossil hominin specimens studied, 16 have carious lesions, six of which are described for the first time in this study. These are from a minimum of six individuals, and include fourP. robustus,oneH. naledi,and oneearly Homoindividual. No carious lesions were found on deciduous teeth, or any teeth assigned toA. africanus. Most are located interproximal, and only posterior teeth are affected. Caries frequency typically ranges between 1-5% of teeth in non-agricultural human samples, and this pattern seemingly holds true for at least the past two million years in the hominin lineage. Non-agricultural populations significantly above or below this threshold generally have a specialized diet, supporting other dietary evidence thatA. africanuslikely consumed large amounts of tough, non-cariogenic vegetation. Given the common occurrence of caries in the other hominin species, cariogenic bacteria and foods were evidently common in their collective oral environment. Along with recent research highlighting additional examples of caries inH. neanderthalensis, earlyHomoand PleistoceneH. sapiens, caries is clearly an ancient disease that was much more common than once maintained throughout the course of human evolution.