bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glial gene networks associated with alcohol dependence
Authors: Erickson Emma K. , Blednov Yuri A. , Harris R. Adron , Mayfield R. Dayne 
Published: July 2019

AbstractChronic alcohol abuse alters the molecular structure and function of brain cells. Recent work suggests adaptations made by glial cells, such as astrocytes and microglia, regulate physiological and behavioral changes associated with addiction. Defining how alcohol dependence alters the transcriptome of different cell types is critical for developing the mechanistic hypotheses necessary for a nuanced understanding of cellular signaling in the alcohol-dependent brain. We performed RNA-sequencing on total homogenate and glial cell populations isolated from mouse prefrontal cortex (PFC) following chronic intermittent ethanol vapor exposure (CIE). Compared with total homogenate, we observed unique and robust gene expression changes in astrocytes and microglia in response to CIE. Gene co-expression network analysis revealed biological pathways and hub genes associated with CIE in astrocytes and microglia that may regulate alcohol-dependent phenotypes. Astrocyte identity and synaptic calcium signaling genes were enriched in alcohol-associated astrocyte networks, while TGF-β signaling and inflammatory response genes were disrupted by CIE treatment in microglia gene networks. Genes related to innate immune signaling, specifically interferon pathways, were consistently up-regulated across CIE-exposed astrocytes, microglia, and total homogenate PFC tissue. This study illuminates the cell-specific effects of chronic alcohol exposure and provides novel molecular targets for studying alcohol dependence.
Similarity index for intuitive assessment of three-dimensional facial asymmetry
Authors: Kwon Sun Mi , Hwang Jae Joon , Jung Yun-Hoa , Cho Bong-Hae , Lee Kee-Joon , Hwang Chung-Ju , Choi Sung-Hwan 
Published: July 2019

AbstractEvaluation of facial asymmetry generally involves landmark-based analyses that cannot intuitively assess differences in three-dimensional (3D) stereoscopic structures between deviation and non-deviation sides. This study tested a newly developed similarity index that uses a mirroring technique to intuitively evaluate 3D mandibular asymmetry, and characterised the resulting lower facial soft tissue asymmetry. The similarity index was used to evaluate asymmetry before and after surgery in 46 adult patients (27 men, 19 women; age, 22 ± 4.8 years) with skeletal Class III malocclusion and facial asymmetry who underwent conventional bimaxillary orthognathic surgery. Relative to the midsagittal plane used as the reference plane, the non-overlapping volume of the mandible significantly decreased, and the similarity index significantly increased after surgery. Similarity indexes of the mandible and lower facial soft tissue were strongly negatively correlated with non-overlapping volumes of each measurement. Differences in bilateral hemi-mandibular and hemi-lower facial soft tissue surface and volume measurements before surgery were significantly negatively correlated with similarity indexes of the mandible before and after surgery. This newly developed similarity index and non-overlapping volume using a mirroring technique can easily and intuitively evaluate overall 3D morphological discrepancies, especially 3D mandibular asymmetry, before and after surgery in skeletal Class III patients with facial asymmetry.
Night-shift work, circadian and melatonin pathway related genes and their interaction on breast cancer risk: evidence from a case-control study in Korean women
Authors: Pham Thu-Thi , Lee Eun-Sook , Kong Sun-Young , Kim Jeongseon , Kim Sun-Young , Joo Jungnam , Yoon Kyong-Ah , Park Boyoung 
Published: July 2019

AbstractOur purpose is to investigate the impact of circadian and melatonin pathway genes as well as their interactions with night-shift work (NSW) on breast cancer risk in Korean women. Information about NSW and other covariates was collected using a structured questionnaire and twenty-two polymorphisms in 11 genes were analyzed in a hospital-based case-control study with 941 cases of breast cancer and 959 controls. In analysis of the main effects of each single nucleotide polymorphisms(SNPs), variants in CLOCK rs11133373 was associated with breast cancer risk even after false discovery rate (FDR) correction (Odd Ratios (OR) = 1.38 (95% Confident Interval (CI) 1.14–1.69) in CG and CC compared to GG genotype. Analysis of MTNR1A rs2119882 demonstrated a decreased risk of breast cancer in CC compared to TT (p-FDR = 0.043). A correlation between NSW and breast cancer interaction was found in two loci. NSW increased risk of breast cancer in women who carried the heterozygote genotype of CRY2 rs2292912 (OR = 1.98, 95% CI = 1.14–3.44) or carried at least one minor allele of RORA rs1482057 (OR = 2.20, 95% CI = 1.10–4.37). Our study results support a putative role for several loci of circadian genes and genes of melatonin biosynthesis and their interaction, and the gene interactions with NSW in the development of breast cancer.
Catalytically Competent Non-transforming H-RASG12P Mutant Provides Insight into Molecular Switch Function and GAP-independent GTPase Activity of RAS
Authors: Ilter Metehan , Sensoy Ozge 
Published: July 2019

AbstractRAS mutants have been extensively studied as they are associated with development of cancer; however, H-RASG12P mutant has remained untouched since it does not lead to transformation in the cell. To the best of our knowledge, this is the first study where structural/dynamical properties of H-RASG12P have been investigated -in comparison to H-RASWT, H-RASG12D, RAF-RBD-bound and GAP-bound H-RASWT- using molecular dynamics simulations (total of 9 μs). We observed remarkable differences in dynamics of Y32. Specifically, it is located far from the nucleotide binding pocket in the catalytically-active GAP-bound H-RASWT, whereas it makes close interaction with the nucleotide in signaling-active systems (H-RASG12D, KRAS4BG12D, RAF-RBD-bound H-RASWT) and H-RASWT. The accessibility of Y32 in wild type protein is achieved upon GAP binding. Interestingly; however, it is intrinsically accessible in H-RASG12P. Considering the fact that incomplete opening of Y32 is associated with cancer, we propose that Y32 can be targeted by means of small therapeutics that can displace it from the nucleotide binding site, thus introducing intrinsic GTPase activity to RAS mutants, which cannot bind to GAP. Therefore, mimicking properties of H-RASG12P in RAS-centered drug discovery studies has the potential of improving success rates since it acts as a molecular switch per se.
In vivo direct reprogramming of glial linage to mature neurons after cerebral ischemia
Authors: Yamashita Toru , Shang Jingwei , Nakano Yumiko , Morihara Ryuta , Sato Kota , Takemoto Mami , Hishikawa Nozomi , Ohta Yasuyuki , Abe Koji 
Published: July 2019

AbstractThe therapeutic effect of in vivo direct reprogramming on ischemic stroke has not been evaluated. In the present study, a retroviral solution (1.5–2.0 × 107 /ul) of mock pMX-GFP (n = 13) or pMX-Ascl1/Sox2/NeuroD1 (ASN) (n = 14) was directly injected into the ipsilateral striatum and cortex 3 days after 30 min of transient cerebral ischemia. The reprogrammed cells first expressed neuronal progenitor marker Dcx 7 and 21 days after viral injection, then expressed mature neuronal marker NeuN. This was accompanied by morphological changes, including long processes and synapse-like structures, 49 days after viral injection. Meanwhile, therapeutic improvement was not detected both in clinical scores or infarct volume. The present study provides a future novel self-repair strategy for ischemic stroke with beneficial modifications of the inducer-suppressor balance.
Population variability of rhesus macaque (Macaca mulatta) NAT1 gene for arylamine N-acetyltransferase 1: Functional effects and comparison with human
Authors: Boukouvala Sotiria , Chasapopoulou Zoi , Giannouri Despina , Kontomina Evanthia , Marinakis Nikolaos , Rizou Sophia V. , Stefani Ioanna , Tsirka Theodora , Veyssière Charlotte , Zaliou Sofia , Sabbagh Audrey , Crouau-Roy Brigitte , Fakis Giannoulis 
Published: July 2019

AbstractHuman NAT1 gene for N-acetyltransferase 1 modulates xenobiotic metabolism of arylamine drugs and mutagens. Beyond pharmacogenetics, NAT1 is also relevant to breast cancer. The population history of human NAT1 suggests evolution through purifying selection, but it is unclear whether this pattern is evident in other primate lineages where population studies are scarce. We report NAT1 polymorphism in 25 rhesus macaques (Macaca mulatta) and describe the haplotypic and functional characteristics of 12 variants. Seven non-synonymous single nucleotide variations (SNVs) were identified and experimentally demonstrated to compromise enzyme function, mainly through destabilization of NAT1 protein and consequent activity loss. One non-synonymous SNV (c.560G > A, p.Arg187Gln) has also been characterized for human NAT1 with similar effects. Population haplotypic and functional variability of rhesus NAT1 was considerably higher than previously reported for its human orthologue, suggesting different environmental pressures in the two lineages. Known functional elements downstream of human NAT1 were also differentiated in rhesus macaque and other primates. Xenobiotic metabolizing enzymes play roles beyond mere protection from exogenous chemicals. Therefore, any link to disease, particularly carcinogenesis, may be via modulation of xenobiotic mutagenicity or more subtle interference with cell physiology. Comparative analyses add the evolutionary dimension to such investigations, assessing functional conservation/diversification among primates.
Strategies and limitations in app usage and human mobility
Authors: De Nadai Marco , Cardoso Angelo , Lima Antonio , Lepri Bruno , Oliver Nuria 
Published: July 2019

AbstractCognition has been found to constrain several aspects of human behaviour, such as the number of friends and the number of favourite places a person keeps stable over time. This limitation has been empirically defined in the physical and social spaces. But do people exhibit similar constraints in the digital space? We address this question through the analysis of pseudonymised mobility and mobile application (app) usage data of 400,000 individuals in a European country for six months. Despite the enormous heterogeneity of apps usage, we find that individuals exhibit a conserved capacity that limits the number of applications they regularly use. Moreover, we find that this capacity steadily decreases with age, as does the capacity in the physical space but with more complex dynamics. Even though people might have the same capacity, applications get added and removed over time. In this respect, we identify two profiles of individuals: app keepers and explorers, which differ in their stable (keepers) vs exploratory (explorers) behaviour regarding their use of mobile applications. Finally, we show that the capacity of applications predicts mobility capacity and vice-versa. By contrast, the behaviour of keepers and explorers may considerably vary across the two domains. Our empirical findings provide an intriguing picture linking human behaviour in the physical and digital worlds which bridges research studies from Computer Science, Social Physics and Computational Social Sciences.
New Absorbable Microvascular Anastomotic Devices Representing a Modified Sleeve Technique: Evaluation of Two Types of Source Material and Design
Authors: Jeong Woonhyeok , Kim Kyuhee , Son Daegu , Kim Yunkun 
Published: July 2019

AbstractThe purpose of this study was to create a new absorbable vascular anastomotic coupler and evaluate the patency and degradation degree. Vascular anastomosis was performed in the jugular vein in 31 New Zealand white female rabbits. The coupler consisted of an inner and outer ring. One side of the jugular vein was passed through and overlapped the inner ring. The opposite side of the jugular vein overlapped the everted jugular vein on the inner ring. Then, the outer ring engaged with the inner ring and completed the anastomosis. The outer rings were also constructed with two shapes including an O-type that had no slit and a C-type with a slit on the outer ring of the O-type coupler to allows expandability of the diameter. A Phase I experiment was performed to evaluate the degradability of the source materials, including the poly (lactic-co-glycolic acid) (PLGA) and polycaprolactone (PCL) couplers. A Phase II experiment was performed to evaluate the patency and anastomosis time of the O-type PLGA and PCL couplers. A Phase III experiment was performed to evaluate the patency and anastomosis time of suture anastomosis (control) and the C-type PLGA coupler. The patency was determined by ultrasonography and open exploration. Histological analysis was performed to determine the degradability of the couplers. In Phase I, the PLGA couplers were completely degraded with good vascular wall remodeling at 8 months, while the PCL couplers demonstrated incomplete degradation. In Phases II and III, the anastomosis time was significantly shorter in the coupler groups than that in the control group. All of the coupler groups demonstrated complete patency of the anastomoses on ultrasonography. In Phase III, the C-type PLGA coupler also demonstrated patency and complete degradation at 8 months. PLGA is a suitable source material for absorbable couplers due to its fast degradability. We devised the O-shaped outer ring for the C-shaped outer ring to increase flexibility, which also demonstrated complete patency during the experimental period. Our absorbable microvascular anastomosis devices could provide rapid and reliable microvascular anastomosis without anastomotic failure.
Magnetic Order with Fractionalized Excitations in Pyrochlore Magnets with Strong Spin-Orbit Coupling
Authors: Chern Li Ern , Kim Yong Baek 
Published: July 2019

AbstractA recent inelastic neutron scattering experiment on the pyrochlore magnet Yb2Ti2O7 uncovers an unusual scattering continuum in the spin excitation spectrum despite the splayed ferromagnetic order in the ground state. While there exist well defined spin wave excitations at high magnetic fields, the one magnon modes and the two magnon continuum start to strongly overlap upon decreasing the field, and eventually they become the scattering continuum at zero field. Motivated by these observations, we investigate the possible emergence of a magnetically ordered ground state with fractionalized excitations in the spin model with the exchange parameters determined from two previous experiments. Using the fermionic parton mean field theory, we show that the magnetically ordered state with fractionalized excitations can arise as a stable mean field ground state in the presence of sufficiently strong quantum fluctuations. The spin excitation spectrum in such a ground state is computed and shown to have the scattering continuum. Upon increasing the field, the fractionalized magnetically ordered state is suppressed, and is eventually replaced by the conventional magnetically ordered phase at high fields, which is consistent with the experimental data. We discuss further implications of these results to the experiments and possible improvements on the theoretical analysis.
Characterization of genes in guar gum biosynthesis based on quantitative RNA-sequencing in guar bean (Cyamopsis tetragonoloba)
Authors: Hu Haiyan , Wang Haijie , Zhang Yaoyuan , Kan Baolin , Ding Yuanhao , Huang Jiaquan 
Published: July 2019

AbstractGuar gum is an important raw material in the food, textile and oil industries, but the biosynthesis of guar gum remains unclear. To illuminate the genes involved in guar gum biosynthesis, guar beans from 30 and 40 days after flowering (DAF) were used for RNA sequencing in this study. A total of 2,535 and 2,724 preferentially expressed genes were found in 30 and 40 DAF endosperm, and 3,720 and 2,530 preferentially expressed genes were found in 30 and 40 DAF embryos, respectively. Of these, mannan synthase genes, α-galactosyltransferase genes and cellulose synthase genes were preferentially expressed in the endosperm from 30 and 40 DAF. The high expression level of these glycometabolism genes in endosperm is consistent with the expectation that the main component of guar gum is galactomannan. We believe that genes related to guar gum biosynthesis found in this study will be useful for both new variety development via genetic engineering and synthetic biology research on guar gum biosynthesis in the future.
From curved spacetime to spacetime-dependent local unitaries over the honeycomb and triangular Quantum Walks
Authors: Arrighi Pablo , Di Molfetta Giuseppe , Marquez-Martin Ivan , Perez Armando 
Published: July 2019

AbstractA discrete-time Quantum Walk (QW) is an operator driving the evolution of a single particle on the lattice, through local unitaries. In a previous paper, we showed that QWs over the honeycomb and triangular lattices can be used to simulate the Dirac equation. We apply a spacetime coordinate transformation upon the lattice of this QW, and show that it is equivalent to introducing spacetime-dependent local unitaries —whilst keeping the lattice fixed. By exploiting this duality between changes in geometry, and changes in local unitaries, we show that the spacetime-dependent QW simulates the Dirac equation in (2 + 1)–dimensional curved spacetime. Interestingly, the duality crucially relies on the non linear-independence of the three preferred directions of the honeycomb and triangular lattices: The same construction would fail for the square lattice. At the practical level, this result opens the possibility to simulate field theories on curved manifolds, via the quantum walk on different kinds of lattices.
Bidirectional optogenetic modulation of prefrontal-hippocampal connectivity in pain-related working memory deficits
Authors: Cardoso-Cruz Helder , Paiva Pedro , Monteiro Clara , Galhardo Vasco 
Published: July 2019

AbstractDysfunction of the prefrontal-hippocampal circuit has been identified as a leading cause to pain-related working-memory (WM) deficits. However, the underlying mechanisms remain poorly determined. To address this issue, we implanted multichannel arrays of electrodes in the prelimbic cortex (PL-mPFC), and in the dorsal hippocampal CA1 field (dCA1) to record the neural activity during the performance of a delayed non-match to sample (DNMS) task. The prefrontal-hippocampal connectivity was selectively modulated by bidirectional optogenetic inhibition or stimulation of local PL-mPFC glutamatergic calcium/calmodulin-dependent protein kinase-II alpha (CaMKIIα) expressing neurons during the DNMS task delay-period. The within-subject behavioral performance was assessed using a persistent neuropathic pain model – spared nerve injury (SNI). Our results showed that the induction of the neuropathic pain condition affects the interplay between PL-mPFC and dCA1 regions in a frequency-dependent manner, and that occurs particularly across theta oscillations while rats performed the task. In SNI-treated rats, this disruption was reversed by the selective optogenetic inhibition of PL-mPFC CaMKIIα-expressing neurons during the last portion of the delay-period, but without any significant effect on pain responses. Finally, we found that prefrontal-hippocampal theta connectivity is strictly associated with higher performance levels. Together, our findings suggest that PL-mPFC CaMKIIα-expressing neurons could be modulated by painful conditions and their activity may be critical for prefrontal-hippocampal connectivity during WM processing.
Minimally Invasive Plate Osteosynthesis Using Fracture Reduction Under the Plate without Intraoperative Fluoroscopy to Stabilize Diaphyseal Fractures of the Tibia and Femur in Dogs and Cats
Authors: Cabassu Julien 
Published: July 2019

Objective The aim of this study was to prospectively evaluate postoperative alignment when using fracture reduction under the plate (FRUP) during a minimally invasive plate osteosynthesis in tibial and femoral fractures, without intraoperative imaging, and report immediate postoperative complications.
Materials and Methods After precise plate contouring and preoperative planning, FRUP was obtained with one cortical screw per fragment. Fractures were stabilized with a plate or plate rod. Tibial/femoral lengths, tibial plateau angles, mechanical medial proximal and distal tibial angles, anatomical lateral distal femoral angles, femoral curvatum and neck anteversion were evaluated on postoperative radiographs and contralateral bone. Tibial torsion was evaluated visually. Paired t-test were used to compare data. Immediate postoperative complications were recorded.
Results Twenty-one tibial and 20 femoral fractures were stabilized (14 plate rod cases). Mean postoperative operated tibial length was 1.4% shorter (p = 0.001). Mean postoperative operated femoral length was 2% shorter (p = 0.04). Mean operated tibial plateau angle was 1.1° lower (p = 0.02). No difference in tibial torsion was noticed. No significant difference in mechanical medial proximal tibial angle, mechanical medial distal tibial angle, anatomical lateral distal femoral angle and femoral neck anteversion was observed. Mean operated femoral curvatum angle was 5.6° less (p = 0.01). Five cases (3 plate rod cases) required an immediate revision.
Clinical Significance Minimally invasive plate osteosynthesis with FRUP leads to acceptable postoperative alignment. Correct pin placement should be evaluated.
Antibiotic Treatments and Patient Outcomes in Necrotizing Enterocolitis
Authors: Murphy Catherine , Nair Jayasree , Wrotniak Brian , Polischuk Emily , Islam Shamim 
Published: July 2019

Abstract
Objective This study aimed to examine the impact of different antibiotic treatments on necrotizing enterocolitis (NEC) outcomes.
Study Design Patient outcomes, including total parenteral nutrition and hospitalization durations, abdominal surgeries, intestinal strictures, and mortality data, were analyzed and compared by various antibiotic groups and treatment durations for 160 NEC patients managed at the Women and Children's Hospital of Buffalo between 2008 and 2016.
Results Fourteen different antibiotics were used for NEC, most commonly ampicillin, gentamicin, and metronidazole (AGM). Medical (vs. surgical) NEC patients more likely received AGM (37 vs. 6%, p < 0.001). Surgical (vs. medical) NEC patients more likely received vancomycin (80 vs. 30%, p < 0.001) and antipseudomonal agents (69 vs. 15%, p < 0.001). For medical NEC there were no outcome differences between patients receiving only AGM versus those receiving other treatments; in patients receiving AGM, there were no outcome differences in durations of ≤10 days versus longer courses.
Conclusion Antibiotic use for NEC varies substantially without definite outcome differences. Particularly with medical NEC, AGM for ≤10 days had comparable outcomes to other treatments. In light of growing concern for short and longer term adverse effects with early-life antibiotic exposure, narrow-spectrum and shorter course NEC treatment may be preferred.