bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Lactic Acid Bacteria Fermentation on Organic Acids, Volatile Aroma Components, and Sensory Quality of Hawthorn Pulp
Authors: Wang Haoyu , Huang Yan , Zhu Chuanhe 
Published: June 2019

Abstract
The purpose of this paper is to investigate the effects of lactic acid bacteria (LAB) fermentation on the volatile aroma components and sensory qualities of hawthorn pulp (HP). High performance liquid chromatography (HPLC) and electrons Nasal combined with HS-SPME-GC-MS were used to analyze the effects of lactic acid bacteria fermentation on the organic acid content and volatile compounds of hawthorn pulp (HP). The results showed that the content and type of organic acids and volatile compounds in HP were significantly improved after fermentation of lactic acid bacteria, and the sensory score was also significantly increased.
Experimental Study of Electrochemical Micro-milling of Silicon
Authors: Hui Chen 
Published: June 2019

AbstractElectrochemical machining (ECM) is a common method of silicon micromachining, but it is difficult to be directly used for three-dimensional processing. Therefore a new electrochemical micro-milling (ECMM) method is proposed. The method combined electrochemical machining and milling processes technology. Micro-removal of materials can be achieved by electrochemical machining technique, while milling processes enable three-dimensional machining. ECMM utilizes the passivation of silicon in sodium hydroxide solution to reduce electrochemical stray corrosion and improve processing accuracy. Experiments showed that the ECMM technology can limit the electrochemical stray corrosion to less than 10 μm. This method can be used for the machining of tiny three-dimensional structures of silicon materials.
Suggestions on Promoting China’s Energy Sustainable Development in the New Era
Authors: Chongxi He , Jie Gu 
Published: June 2019

Abstract
China is a major energy producer and a big consumer in the world. However, with the constraints of traditional energy shortages and energy security factors and the enhancement of Chinese people ecological and environmental protection concepts, the sustainable development of energy and the use of sustainable energy are receiving more and more attention. This paper will systematically analyze the current status and existing problems of China’s current energy development in the new era of socialism, and propose a series of targeted recommendations for sustainable energy development.
Effects of Relative Humidity on Impregnated Filters Used in Measurement of Airborne Sulfur Dioxide
Authors: Chien Chih-Hsiang , Zhou Chufan , Sing Simon Yang , Lopez Benjamin , Theodore Alexandros , Wu Chang-Yu , Birky Brian K 
Published: June 2019

Abstract
Impregnated filters treated with alkali and humectant were first used as collection media to assess occupational exposure to sulfur dioxide (SO2), as outlined in the National Institute for Occupational Safety and Health Method 6004 in 1979. Since then, updated treatment protocols have been proposed with decreased amounts of alkali and glycerol, which claim the same filtering capacity. However, there has been no report on how the collection of SO2 on such impregnated media is influenced by relative humidity (RH). This study investigated the role of glycerol (G) amount on impregnated filters (G2 and G10, referring to 2 and 10% glycerol, respectively) in the collection of SO2 (100 l of 10 ppm at 1 l per minute) under low, medium, and high RHs. The testing results show that RH significantly impacted G2 filters with respect to breakthrough time, capacity, and recovery. At low RH, the 5% breakthrough time was less than 10 min and its recovery was merely 42%; at medium and high RHs, although the recovery was satisfactory, the 5% breakthrough time was still less than 100 min. By contrast, G10 filters illustrated nearly 100% recovery and evaluation by analysis of variance showed no significant effect of RH on recovery. In summary, the current treatment protocol of 2% glycerol leads to a significant underestimation of the exposure to SO2 in a low-RH environment; increasing the glycerol content can be an effective alternative to compensating for the effect of RH.
Parental care buffers against effects of ambient temperature on offspring performance in an insect
Authors: Grew Richard , Ratz Tom , Richardson Jon , Smiseth Per T 
Published: June 2019

AbstractUnderstanding how animals respond to and cope with variation in ambient temperature is an important priority. The reason for this is that ambient temperature is a key component of the physical environment that influences offspring performance in a wide range of ectotherms and endotherms. Here, we investigate whether posthatching parental care provides a behavioral mechanism for buffering against the effects of ambient temperature on offspring in the burying beetle Nicrophorus vespilloides. We used a 3 × 2 factorial design where we manipulated ambient temperature (15, 20, or 25 °C) and parental care (presence or absence of a female parent after hatching). We found that the effect of ambient temperature on offspring performance was conditional upon the presence or absence of a caring female. Fewer larvae survived in the absence than in the presence of a caring female at 15 °C while there was no difference in larval survival at 20 and 25 °C. Our results show that parental care buffers against some of the detrimental effects of variation in ambient temperature on offspring. We suggest that posthatching parental care may buffer against such effects by creating a more benign environment or by boosting offspring resilience toward stressors. Our results have important implications for our understanding of the evolution of parental care because they suggest that the evolution of parental care could allow species to expand their geographical range to colonize areas with harsher climatic conditions than they otherwise would tolerate.
Self-deception in nonhuman animals: weak crayfish escalated aggression as if they were strong
Authors: Angilletta Michael J , Kubitz Gregory , Wilson Robbie S 
Published: June 2019

AbstractHumans routinely deceive themselves when communicating to others, but no one knows whether other animals do the same. We ask whether dishonest signaling between crayfish meets a condition required for self-deception: dishonest individuals and honest individuals escalate aggression according to their signals of strength rather than actual strength. Using game theory, we predicted how an animal’s knowledge of its strength should affect its decision to escalate aggression. At the evolutionary equilibrium, an animal that knows its strength should escalate aggression according to its strength, relative to the expected strength of its opponent. By contrast, an animal that knows only its size should escalate aggression according to its size, relative to the size of its opponent. We tested these predictions by staging encounters between male crayfish (Cherax dispar) of known sizes and strengths. Consistent with a model of self-deception, crayfish escalated aggression based on the sizes of their claws relative to those of their opponents, despite the fact that size poorly predicts strength. Males who were weak for their size escalated disputes less often, but their aggression far exceeded the level predicted by a model of self-awareness, suggesting these crayfish were largely ignorant of their deception. Animals that fail to recognize their own dishonest signals may win disputes with stronger opponents without engaging in costly combat. Our game-theoretical approach can be used to identify potential cases of self-deception in nonhuman animals, enabling comparative studies of this behavior.
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding
Authors: Zeng Haoyang , Gifford David K 
Published: June 2019

Abstract

Motivation
The computational modeling of peptide display by class I major histocompatibility complexes (MHCs) is essential for peptide-based therapeutics design. Existing computational methods for peptide-display focus on modeling the peptide-MHC-binding affinity. However, such models are not able to characterize the sequence features for the other cellular processes in the peptide display pathway that determines MHC ligand selection.

Results
We introduce a semi-supervised model, DeepLigand that outperforms the state-of-the-art models in MHC Class I ligand prediction. DeepLigand combines a peptide language model and peptide binding affinity prediction to score MHC class I peptide presentation. The peptide language model characterizes sequence features that correspond to secondary factors in MHC ligand selection other than binding affinity. The peptide embedding is learned by pre-training on natural ligands, and can discriminate between ligands and non-ligands in the absence of binding affinity prediction. Although conventional affinity-based models fail to classify peptides with moderate affinities, DeepLigand discriminates ligands from non-ligands with consistently high accuracy.

Availability and implementation
We make DeepLigand available at https://github.com/gifford-lab/DeepLigand.

Supplementary information
Supplementary data are available at Bioinformatics online.
Preeclampsia may influence offspring neuroanatomy and cognitive function: a role for placental growth factor†
Authors: Kay Vanessa R , Rätsep Matthew T , Figueiró-Filho Ernesto A , Croy B Anne 
Published: June 2019

AbstractPreeclampsia (PE) is a common pregnancy complication affecting 3–5% of women. Preeclampsia is diagnosed clinically as new-onset hypertension with associated end organ damage after 20 weeks of gestation. Despite being diagnosed as a maternal syndrome, fetal experience of PE is a developmental insult with lifelong cognitive consequences. These cognitive alterations are associated with distorted neuroanatomy and cerebrovasculature, including a higher risk of stroke. The pathophysiology of a PE pregnancy is complex, with many factors potentially able to affect fetal development. Deficient pro-angiogenic factor expression is one aspect that may impair fetal vascularization, alter brain structure, and affect future cognition. Of the pro-angiogenic growth factors, placental growth factor (PGF) is strongly linked to PE. Concentrations of PGF are inappropriately low in maternal blood both before and during a PE gestation. Fetal concentrations of PGF appear to mirror maternal circulating concentrations. Using Pgf−/− mice that may model effects of PE on offspring, we demonstrated altered central nervous system vascularization, neuroanatomy, and behavior. Overall, we propose that development of the fetal brain is impaired in PE, making the offspring of preeclamptic pregnancies a unique cohort with greater risk of altered cognition and cerebrovasculature. These individuals may benefit from early interventions, either pharmacological or environmental. The early neonatal period may be a promising window for intervention while the developing brain retains plasticity.
Purification of specific DNA species using the CRISPR system
Authors: Fujita Toshitsugu , Fujii Hodaka 
Published: June 2019

AbstractIn 2013, we developed a new method of engineered DNA-binding molecule-mediated chromatin immunoprecipitation that incorporates the clustered regularly interspaced short palindromic repeats (CRISPR) system to purify specific DNA species. This CRISPR-mediated purification can be performed in-cell or in vitro; CRISPR complexes can be expressed to tag target DNA sequences in the cells to be analyzed, or a CRISPR ribonucleoprotein complex consisting of recombinant nuclease-dead Cas9 (dCas9) and synthetic guide RNA can be used to tag target DNA sequences in vitro. Both methods enable purification of specific DNA sequences in chromatin structures for subsequent identification of molecules (proteins, RNAs, and other genomic regions) associated with the target sequences. The in vitro method also enables enrichment of purified DNA sequences from a pool of heterogeneous sequences for next-generation sequencing or other applications. In this review, we outline the principle of CRISPR-mediated purification of specific DNA species and discuss recent advances in the technology.
Natural hybridization patterns between widespread Calanthe discolor (Orchidaceae) and insular Calanthe izu-insularis on the oceanic Izu Islands
Authors: Nakahama Naoyuki , Suetsugu Kenji , Ito Azusa , Hino Masayuki , Yukawa Tomohisa , Isagi Yuji 
Published: June 2019

AbstractNatural hybridization often occurs between insular and widespread species, and investigating these hybridization patterns is important in improving our understanding of the evolution of insular plant species. To this end, we studied the floral morphology and genetic structure of the widespread species Calanthe discolor, the insular closely related species C. izu-insularis and their putative natural hybrids on Honshu Island (mainland) and the Izu Islands (oceanic islands), Japan, using microsatellite markers. Natural hybridization probably occurred on all the investigated Izu Islands in Japan, although C. izu-insularis was morphologically and genetically different from C. discolor. Bumblebees and other relatively large bees are not distributed in the Izu Islands and therefore natural hybridization would have occurred via pollination by relatively small solitary bees that are pollinators of both Calanthe spp. We also showed that in the islands more remote from the mainland, the proportions of insular C. izu-insularis increased and the floral morphologies of both species changed. The results suggested that insular C. izu-insularis evolved on the Izu Islands and the widespread C. discolor adapted to the poor pollinator fauna on oceanic islands.
Is 3D Dobutamine stress echocardiography ready for prime time? Diagnostic and prognostic implications
Authors: Shivalkar Bharati , De Keersmaeker Alexander , Van Hoeck Nathan , Belkova Petra , Van de Heyning Caroline M , De Maeyer Catherine , Vrints Christiaan 
Published: June 2019

Abstract

Aims
Compare the diagnostic accuracy and prognostic value of echo contrast enhanced 2D and 3D Dobutamine stress echocardiography (DSE).

Methods and results
We included 718 patients indicated for DSE. All had standard 2D, and contrast enhanced left ventricular opacification (LVO) for 2D and 3D acquisitions at rest and peak stress. Chi-square test was done to assess relationship between DSE result and early revascularization. Kaplan–Meier plots with Logistic regression analysis predicted late major adverse cardiovascular events (MACE) at a maximum follow-up of 84 months. The mean age was 63 ± 13 years (61% males) and follow-up was obtained in 692/718 (96.4%) patients. Only 32% had excellent baseline image quality. The DSE was abnormal in 19.4% patients on 2D, in 17.1% on 2D-LVO and in 19.1% on 3D-LVO. Early revascularization was performed in, respectively, 32.8%, 45.8%, and in 48.5% of stress-positive 2D, 2D-LVO, and 3D-LVO studies. After excluding the 66 patients receiving early revascularization 68/626 (10.9%) had MACE at a maximum follow-up of 84 months. Kaplan–Meier plots showed that stress-positive 2D-LVO and 3D-LVO studies not receiving early revascularization when assessed separately and combined had significantly worse outcomes for MACE compared with stress-negative patients (OR 3.69; 95% CI: 1.54–8.87; P = 0.011, OR 4.54; 95% CI: 1.72–12.93; P = 0.008, and OR 7.07, 95% CI: 1.62–25.16; P = 0.001, respectively).

Conclusion
Combined use of 2D- and 3D-LVO DSE is ready for prime time considering the feasibility, improved diagnostic accuracy and prognostic value.
Updates to the Symbol Nomenclature for Glycans guidelines
Authors: Neelamegham Sriram , Aoki-Kinoshita Kiyoko , Bolton Evan , Frank Martin , Lisacek Frederique , Lütteke Thomas , O’Boyle Noel , Packer Nicolle
H , Stanley Pamela , Toukach Philip , Varki Ajit , Woods Robert J ,   The SNFG Discussion Group, Darvill Alan , Dell Anne , Henrissat Bernard , Bertozzi Carolyn , Hart Gerald , Narimatsu Hisashi , Freeze Hudson , Yamada Issaku , Paulson James , Prestegard James , Marth Jamey , Vliegenthart J F G , Etzler Marilynn , Aebi Markus , Kanehisa Minoru , Taniguchi Naoyuki , Edwards Nathan , Rudd Pauline , Seeberger Peter , Mazumder Raja , Ranzinger Rene , Cummings Richard , Schnaar Ronald , Perez Serge , Kornfeld Stuart , Kinoshita Taroh , York William , Knirel Yuriy 
Published: June 2019

Abstract
The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.
Obesity and risk of infections: results from men and women in the Swedish National March Cohort
Authors: Ghilotti Francesca , Bellocco Rino , Ye Weimin , Adami Hans-Olov , Trolle Lagerros Ylva 
Published: June 2019

Abstract

Background
Previous studies have shown an association between body mass index (BMI) and infections, but the literature on type-specific community acquired infections is still limited.

Methods
We included 39 163 Swedish adults who completed a questionnaire in September 1997 and were followed through record-linkages until December 2016. Information on BMI was self-reported and infections were identified from the Swedish National Patient Register using International Classification of Diseases (ICD), Tenth Revision (ICD-10) codes. We fitted multivariable Cox proportional hazards models for time-to-first-event analysis, and we used extensions of the standard Cox model when repeated events were included.

Results
During a 19-year follow-up 32% of the subjects had at least one infection requiring health care contact, leading to a total of 27 675 events. We found an increased incidence of any infection in obese women [hazard ratio (HR) = 1.22; 95% confidence interval (CI) = 1.12; 1.33] and obese men (HR = 1.25; 95% CI = 1.09; 1.43) compared with normal weight subjects. For specific infections, higher incidences were observed for skin infections in both genders (HR = 1.76; 95% CI = 1.47; 2.12 for obese females and HR = 1.74; 95% CI = 1.33; 2.28 for obese males) and gastrointestinal tract infections (HR = 1.44; 95% CI = 1.19; 1.75), urinary tract infections (HR = 1.30; 95% CI = 1.08; 1.55) and sepsis (HR = 2.09; 95% CI = 1.46; 2.99) in obese females. When accounting for repeated events, estimates similar to the aforementioned ones were found.

Conclusions
Obesity was associated with an increased risk of infections in both genders. Results from multiple-failure survival analysis were consistent with those from classic Cox models.
Folic acid supplementation and risk for congenital limb reduction defects in China
Authors: Liu Jufen , Li Zhiwen , Ye Rongwei , Ren Aiguo , Liu Jianmeng 
Published: June 2019

Abstract

Background
Folic acid (FA) supplementation prevents neural tube defects, but there are mixed results for its ability to prevent limb reduction defects. We examined whether a preventive effect of FA supplementation exists for congenital limb reduction defects in a large population in China.

Methods
Data from a large population-based cohort study in China were used to evaluate the effects of FA supplementation on birth defects. All births at 20 complete gestational weeks, including live births, stillbirths and pregnancy terminations, and all structural congenital anomalies, regardless of gestational week, were recorded. A total of 247 831 singleton live births delivered at gestational ages of 20–42 weeks to women from northern and southern China with full information on FA intake were included. Limb reduction defects were classified by subtype and maternal FA supplementation.

Results
The prevalence of limb reduction defects was 2.7 per 10 000 births among women who took FA compared with 9.7 per 10 000 births among those who did not take FA in northern China; the prevalence was 4.5 and 3.8 per 10 000 births, respectively, in southern China. In both unadjusted and adjusted analyses, the estimated relative risk for upper limb reduction defects [odds ratio (OR) = 0.17, 95% confidence interval (CI): 0.04, 0.63] and total limb reduction defects (OR = 0.24, 95% CI: 0.08, 0.70) in northern China, but not for lower limb reduction defects ,was significantly decreased in association with FA supplementation in northern China. There was no association between FA supplementation and either an increased or decreased risk for limb reduction defects in southern China.

Conclusions
FA supplementation successfully reduces the prevalence of limb reduction defects in northern China, whose population has low folate concentrations.
Development of a Global Rating Scale for Inflammatory Bowel Disease
Authors: Bitton Alain , Devitt Katharine S , Bressler Brian , Heatherington Joan , Jairath Vipul , Jones Jennifer , Moayyedi Paul , Weizman Adam V , Dubé Catherine , MacIntosh Donald , Nguyen Geoffrey C 
Published: June 2019

Abstract

Background
The Global Rating Scale (GRS) is a web-based self-assessment quality improvement tool used to identify gaps in health care, change the focus to patient-centred care and standardize care. There are four levels of achievement ranging from basic-(D) to excellent-(A) service delivery. The goal was to develop a GRS for inflammatory bowel disease (IBD) to improve the quality of care for patients on a system level.

Methods
The IBD GRS was developed through an iterative process and modeled upon the successful endoscopy GRS programs in the United Kingdom and Canada. Dimensions, items and statements were drafted based on expert opinions, patient-informed quality indicators and best available evidence, then reviewed and modified by a core committee. A working group of IBD and GRS experts voted in-person to establish consensus on the inclusion and quality of statements.

Results
Two dimensions (Clinical Quality and Quality of Patient Experience), 10 items and 89 statements made up the IBD GRS. There was a 100% response rate for each of the 40 votes for statements in the IBD GRS. All statements within each level received a mean rating score between four (agree) and five (strongly agree). Revisions agreed upon during the voting process were incorporated into the IBD GRS. Group consensus was achieved on the inclusion of statements, and 10 items were selected as standards within the two dimensions.

Conclusions
We have developed the first IBD GRS with the aim of improving quality of care through ongoing evaluations and improvements by health care teams, focusing on patient-centred care.