bluuebunny/crossref_metadata_2025 huggingface dataset:
Co-initiation of continuous renal replacement therapy, peritoneal dialysis, and extracorporeal membrane oxygenation in neonatal life-threatening hyaline membrane disease
Authors: Li Guanhua , Zhang Li , Sun Yunxia , Chen Jimei , Zhou Chengbin
Published: January 2019

Rationale:

Extracorporeal membrane oxygenation (ECMO) is a well-known technique to provide cardio-pulmonary support. Although continuous renal replacement therapy (CRRT) is frequently indicated, the need for faster fluid removal as the primary indication for ECMO is uncommon. Experiences on concomitant applications of ECMO, peritoneal dialysis (PD) and CRRT in neonates are relatively limited.

Patient concerns:

We report a 2-day-old male neonate with life-threatening hyaline membrane disease (HMD), accompained by severe systemic fluid retention, sepsis and abdominal compartment syndrome.

Diagnosis:

Hyaline membrane disease (HMD), neonatal respiratory distress syndrome, sepsis, capillary leakage syndrome, and abdominal compartment syndrome.

Intervention:

Veno-arterial ECMO, CRRT, and PD were synchronously initiated for the sake of faster fluid removal possible.

Outcomes:

The infant was successfully weaned from ECMO circuit and fluid overload was greatly improved four days after extracorporeal life support (ECLS), without major complications.

Lessons:

Initiation of CRRT and PD during ECMO therapy is effective and safe to release fluid overload in neonates, and severe complications are absent. When a neonate requires dialysis of urgency, ECMO offers assured vascular access to hemodialysis, allowing faster fluid removal.
Combined treatment with vacuum sealing drainage, TopClosure device, and Ilizarov technique for traumatic hemipelvectomy
Authors: Li Jin , Shi Jie Bao , Hong Pan , Wang Yu Shang , Ze Hao Ren , Lee Rushyuan Jay , Tang Xin
Published: January 2019

Rationale:

Traumatic hemipelvectomy is a rare but lethal catastrophic injury.

Patient concerns:

A case of a very young child with open fracture of left sacroiliac joint dislocation and pubic symphysis diastasis, suffered from a severe large-size soft tissue defects.

Diagnosis:

Traumatic hemipelvectomy.

Interventions:

Complete amputation was performed and three kinds of surgical techniques including regulated negative pressure-assisted wound therapy (RNPT), TopClosure device, and Ilizarov technique were jointly utilized to secure closure in the further revisions of the soft tissue injury and reconstruct reconstructive surgery.

Outcomes:

Six months after hospital discharge, the patient was able to ambulate with a single limb and a prosthesis and she is independent in many activities of daily living currently.

Lessons:

We report this case to share experience with other clinicians in the management of this deadly extensive defects after traumatic hemipelvectomy in patients.
Acupuncture treatment on idiopathic trigeminal neuralgia
Authors: Liu Hao , Li Xin-Wei , Du Jia
Published: January 2019

Introduction:

The objective of this systematic review protocol is to provide the methods for evaluating the effectiveness and safety of acupuncture on the treatment of idiopathic trigeminal neuralgia (ITN).

Methods and analysis:

We will search randomized controlled trials (RCTs) on this subject in 8 electronic databases and they are Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Chinese Biomedical Literature Database (CBM), China National Knowledge Infrastructure (CNKI), the Wan-Fang Database, and Chinese Scientific Journal Database (VIP database). Other relevant literatures will be manually searched as a complement. Only RCTs related to acupuncture for ITN in English or Chinese will be included, without limitation of publication types. The risk of bias and trial quality will be assessed by the Cochrane collaboration's tool. All data will be analyzed by RevMan V.5.3.3 statistical software.

Ethics and dissemination:

Ethical approval is not necessary as this paper does not involve patient data. This protocol will be disseminated by a peer-review journal or conference presentation.

Trial registration number:

PROSPERO CRD42015022173

Strengths and limitations of this study:

This systematic review will evaluate the effectivity and safety of acupuncture treatment on idiopathic trigeminal neuralgia. Two authors will perform independently study selection, data extraction and quality assessment, in order to ensure that all included studies are not personal bias. The result of this systematic review may give clinicians more ways to assist patient in relieving trigeminal neuralgia.

This shortage of systematic review is due to language barriers, only 2 languages of the trials can be included, other related studies may be missing. Different methods of acupuncture and quality of methodologies may result in essential heterogeneity.
Screening of common genetic variants in the APOB gene related to familial hypercholesterolemia in a Saudi population
Authors: Batais Mohammed Ali , Almigbal Turky H. , Shaik Noor Ahmad , Alharbi Fawaziah Khalaf , Alharbi Khalid Khalaf , Ali Khan Imran
Published: January 2019

Familial hypercholesterolemia (FH) is a monogenic dominant inherited disorder of lipid metabolism characterized by elevated low-density lipoprotein levels, and is mainly attributable to mutations in low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proportein convertase subtilisin/kexin type 9 (PCSK9) genes. Next-generation and exome sequencing studies have primarily involved genome-wide association analyses, and meta-analyses and next-generation studies examined a few single-nucleotide polymorphisms (rs151009667 and Val2095Glu) in the ApoB gene. The present study was conducted to investigate the association of APOB and patients with FH in a Saudi population.

We genotyped 100 patients with FH and 100 controls for 2 polymorphisms in APOB using polymerase chain reaction-restriction fragment length polymorphism, followed by 3% agarose gel electrophoresis. The strength of the association between the genotype and allele frequencies with the risk of developing FH was evaluated. Clinical details and genotype analysis results were recorded.

For the rs151009667 polymorphism, 18% of the CT genotypes were observed only in patients with FH. There was a positive association between CT and CC (odds ratio [OR] 45.07 [95% conflict of interest (CI), 2.67–759.1]; P = .0001) and between T and C (OR 87.8 [95% CI, 5.34–144.2]; P < .0001). However, no Val2095Glu mutations were found in patients with FH or controls. There was also no correlation between clinical characteristics and the rs151009667 polymorphism.

In conclusion, we confirmed the association between the rs151009667 polymorphism and FH in a Saudi population. The Val2095Glu novel variant did not appear in either patients with FH or controls. Similar studies should be performed in different ethnic populations to rule out the role of this polymorphism in FH.
Improvement in quality of life of Chinese chronic heart failure patients with neuropsychiatric complications over 12-months post-treatment with metoprolol
Authors: Zhang Ran , Huang Jingjing , Shu Qiuhong , Wu Liyong , Zhang Qian , Meng Yong
Published: January 2019

Psychological disorders, such as depression and anxiety, are known to be associated with chronic heart failure (CHF). The present study was conducted to evaluate the effect of mental status on quality of life (QoL) in metoprolol treated CHF patients with depression, anxiety, and burn-out.

This single-center prospective study was conducted between February 2013 and April 2016, enrolled CHF patients (resting heart rate >80 bpm) with depression, anxiety, and burn out at baseline. Hospital anxiety and depression scale (HADS) and Copenhagen burnout inventory (CBI) were used to assess the depression–anxiety status and burn-out status, respectively. Change in QoL was evaluated as the endpoint at 1st, 3rd, 6th, and 12th month from baseline using Minnesota Living with Heart Failure Questionnaire (MLHFQ) and short form-8 (SF-8) scales. A student t test was used to determine the change and P value < .05 was considered statistically significant. One hundred fifty-four patients were enrolled (median age 66 years; 65.58% males) and divided into 8 groups based on the HADS and CBI scores at baseline. Overall, the mean SF8 score and MLHFQ scores in different mental status groups showed a significant improvement (P < .05) in QoL from baseline to 12th month, with no significant difference reported between the groups. With regard to the follow-up periods, there was a deterioration in QoL until 3rd month, after which there was a significant improvement (P < .05).

There was a significant improvement in QoL in metoprolol treated CHF patients with depression, anxiety, and burn-out.
The association between ambient air pollution and birth defects in four cities in Hunan province, China, from 2014 to 2016
Authors: Xiong Lili , Xu Zenghui , Wang Hua , Liu Zhiyu , Xie Donghua , Wang Aihua , Kong Fanjuan
Published: January 2019

This study was performed to assess whether air pollution was positively associated with birth defects and if a specific pregnancy stage played a role. This was a population-based case-control study comprising 153,822 perinatal births in four cities located in Hunan province, China, during the period 2014 to 2016. Exposure to SO2, NO2, and PM10 in each pregnant woman in the first 3 months before pregnancy, and in the first and third trimester was assessed. The risk of birth defects related to SO2 in the first 3 months before pregnancy was between 1.191 and 1.566. In the first trimester stage the risk was between 1.104 and 1.348. The risk of birth defects related to NO2 before pregnancy was 1.285 (95%CI: 1.180–1.399), in the first trimester stage the risk was between 1.280 (95%CI: 1.197–1.368) and 1.380 (95%CI: 1.293–1.473). In the third month before delivery the risk was 1.484 (95%CI: 1.366–1.613). The risk of birth defects related to PM10 in the first month of pregnancy was 1.098 (95%CI: 1.057–1.140), and in the third month before delivery the risk was 1.296 (95%CI: 1.222–1.375). SO2 had a greater effect on the prophase of pregnancy, while NO2 and PM10 had an effect in the late third trimester.
Pelvic lipomatosis with ureteral calculi managed by flexible ureteroscopy
Authors: Yang Lei , Tang Wei
Published: January 2019

Rationale:

Pelvic lipomatosis (PL) is a benign disease characterized by overgrowth of adipose tissue in pelvic space. Hydronephrosis and ureterectasis are common complications caused by PL in urinary system. But PL accompanied with upper urinary tract calculi is rare. Also there has been no report of PL with ureteral calculi managed by flexible ureteroscopy (fURS).

Patient concerns:

A 62-year-old man who has been diagnosed of PL was found to have a right-side ureteral calculi by ultrasound in the routine health examination. In addition, the patient has a history of open surgery of uretero-vesical reimplantation in the left side 13 years ago because of heavy hydronephrosis in the left side.

Diagnoses:

The diagnosis was PL with ureteral calculi in the right side and heavy hydronephrosis in the left side.

Interventions:

FURS was performed to remove the right ureteral calculi.

Outcomes:

A follow-up of 1 year showed that there was no progression of the hydronephrosis in right side and serum creatinine was stable.

Lessons:

FURS is a suitable option for the upper urinary tract calculi accompanied with anatomical abnormality such as horseshoe kidney, pelvic ectopic kidney and so on. For patient of PL accompanied with upper urinary tract calculi, fURS is suitable and indicated.
Efficacy and safety of herbal medicine (Bailemian capsule) for treating insomnia
Authors: Tian Tian , Hua Lian , Wang Jianxin , Guan Jingzhi
Published: January 2019

Background:

Insomnia has become a universal subhealth disease, affecting more and more modern people's health and quality of life. At present, western medicine is only symptomatic treatment for insomnia. Bailemian Capsule (BLMC) is a proprietary Chinese medicine for treating insomnia. It has been widely used in China, but lacks evidence for evidence-based medicine. At the same time, the clinical efficacy and safety of BLMC are controversial. Therefore, the effectiveness and safety of BLMC in the treatment of insomnia are studied and systematically evaluated in this study. It provides reliable theoretical support for the treatment of insomnia with Traditional Chinese Medicine and the combination of traditional Chinese and Western medicine.

Methods:

The information was retrieved from electronic databases, Cochrane, PubMed, EMBASE, SinoMed, China National Knowledge Infrastructure, VIP Data, and WangFang Data. Randomized controlled trials on the BLMC in the treatment of insomnia were conducted. There was no limitation on the literature language. RevMan 5.3 software and STATA 12.0 software were used to perform the meta-analysis.

Results:

This review will be to assess the efficacy and safety of BLMC for insomnia.

Conclusion:

Our systematic evaluation will provide evidence for the clinical efficacy and safety of BLMC in the treatment of insomnia, and will be published in the form of academic papers in the future to provide new ideas for clinicians in the treatment of insomnia.
Co-outbreak of multidrug resistance and a novel ST3006 Klebsiella pneumoniae in a neonatal intensive care unit
Authors: Chen Dongjie , Hu Xinlan , Chen Falin , Li Hongru , Wang Daxuan , Li Xiaoqin , Wu Changsheng , Li Ning , Wu Shaolian , Li Zhen , Chen Liqing , Chen Yusheng
Published: January 2019

The outbreak of carbapenem-resistant Klebsiella pneumoniae is a serious public health problem, especially in the neonatal intensive care unit (NICU).

Fifteen K. pneumoniae strains were isolated from 7 neonates during June 3 to 28, 2017 in an NICU. Antimicrobial susceptibility was determined by the Vitek 2 system and microbroth dilution method. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to analyze the genetic relatedness of the isolates. Whole-genome sequencing and gene function analysis were performed to investigate pathogenicity and drug resistance and screen genomic islands.

Three clones of K. pneumoniae were identified from 7 neonates: 7 strains of ST37, 7 of novel ST3006, and 1 of ST1224. Gene sequencing showed that the kpn1343 (ST37) strain harbored 12 resistance genes (OXA-33, TEM-1, SHV-11, AAC (6’)-IId, AAC (3)-IIa, AAC (6’)-Ib-cr, catB3, arr-3, sul1, oqxB, oqxA, CRP, and catB3) and included 15 genomic islands and 205 reduced virulence genes. The kpn1344 (ST3006) strain harbored 4 antibiotic-resistant genes (TEM-1, CTX-M-3, vgaC, and CRP) and included 19 genomic islands and 209 reduced virulence genes. MLST and PFGE showed that 15 strains of K. pneumoniae were divided into 3 groups with a high level of homology. ST1224 (kpn1362) was isolated on June 28, 2017, which was 10 days after the last isolate (kpn1359, June 18, 2017); thus, we speculated that ST1224 was not the clone that caused the outbreak.

This co-outbreak of K. pneumoniae involved 2 clones: ST37 and ST3006. ST37 carried the multidrug-resistant genes, such as OXA-33, TEM-1, and SHV-11, and ST3006 was a novel K. pneumoniae ST typing. Whole-genome sequencing may be an effective method for screening bacterial-resistant genes and their functions.
Pregnancy Incidence and Fertility Desires Among Couples by HIV Status in Rakai, Uganda
Authors: Brahmbhatt Heena , Santelli John , Kaagayi Joseph , Lutalo Tom , Serwadda David , Makumbi Frederick
Published: January 2019

Background:

The desire for more children and pregnancy rates are influenced by many relationship dynamics and HIV serostatus of couples.

Setting:

Rakai Community Cohort Study in Uganda.

Methods:

Couple data were retrospectively linked from survey rounds between 2007 and 2015 to assess drivers of fertility desire and pregnancy incidence by HIV status (M−F−; M+F+; M−F+; and M+F−). Multivariable modified Poisson regression was used to estimate prevalence ratios of fertility desire, whereas multivariable Poisson regression was used to estimate incidence rate ratios of pregnancy associated with couple characteristics.

Results:

Six thousand six hundred forty-seven couples contributed to 7656 person-years. Approximately 40% of couples (where at least 1 HIV+) desired more children. Unmet need for family planning was evident; couples of medium or low Socioeconomic status and with coresident children had lower fertility desires but higher pregnancy rates. Older age, being in a polygamous union, and having a HIV+ spouse in care were associated with lower fertility desire while having an older male partner was associated with higher fertility desire. Pregnancy incidence was lower with older age, among women using hormonal contraception and condoms, HIV+ concordant couples and couples where the HIV+ spouse was in care while pregnancy incidence were higher among women who desired more children, and serodiscordant couples (M−F+).

Conclusions:

There are many drivers of fertility desires and pregnancy rates, and HIV does not diminish the desire for more children. Unmet need for family planning was evident and highlighted the need to understand and meet the contraceptive needs of couples.
What Types of Physical Function Predict Program Adherence in Older Adults?
Authors: Liu Minhui , Miyawaki Christina E.
Published: January 2019

Purpose

The aims of this study were to describe participants’ demographic characteristics by adherence levels and to examine the association between participants’ baseline physical function and their adherence to an evidence-based group exercise program.

Design

A prospective exploratory study (N = 36,373).

Methods

Participants’ physical function was assessed using 30-second chair-stand, arm-curl, and 8-foot up-and-go tests. Adherence was calculated as the proportion of attended sessions over offered sessions.

Findings

Participants’ mean adherence was 52%. Older male, Asian/Pacific Islander race, and Washington State residents with fewer chronic conditions showed higher adherence. Multinomial logistic regression showed the baseline 30-second chair-stand, arm-curl, and 8-foot up-and-go tests significantly predict adherence levels after controlling for demographics.

Conclusions

Stronger upper- and lower-extremity strength and better walking balance and mobility are associated with higher adherence to exercise programs in older adults.

Clinical Relevance

The results underscored the importance of offering classes at various physical function levels while considering participants’ individual needs.
Pharmacologic and Exercise Considerations in Older Adults With Diabetes
Authors: Wenker Susan L. , Walbrandt Pigarelli Denise L.
Published: January 2019

Diabetes mellitus affects approximately 25% of United States adults aged 65 years and older, and the disease often complicates the aging process. Diabetes management requires attention to 3 treatment modalities: exercise, medical nutrition therapy, and medications. The main objective when working with patients who have diabetes is to optimize life while providing interventions to minimize organ system impairment, which may cause reduced body function and, subsequently, decreased life participation.
Clinically Relevant Drug-Induced Myopathies
Authors: Burke-Doe Annie
Published: January 2019

Clinically identified myopathies can occur with administration of medications such as statins, glucocorticoids, antibiotics, antirheumatics, and retinoids. While the frequency of drug-induced myopathies is unclear, they are an important group of disorders in anyone presenting with muscular symptoms and should be considered in patients with symptoms ranging from mild myalgia or muscle cramping to profound muscle weakness without a known etiology. Certain medications are commonly associated with myopathy and frequently prescribed (glucocorticoids, statins); a few are more likely to occur with exercise, whereas others have myopathy as a rare side effect. Developing a greater understanding of underlying mechanisms and symptoms of drug-induced myopathy can promote enhanced awareness, early recognition, and improved patient care because many drug-induced myopathies are potentially reversible at early stages.
The Crossroads of Aging
Authors: Severin Richard , Berner Patrick M. , Miller Kenneth L. , Mey Jacob
Published: January 2019

The intersectional relationship between malnutrition, frailty, and sarcopenia in older adults presents unique challenges for health care providers. Malnutrition, specifically, is a leading risk factor for disability, morbidity, and mortality in older adults. Despite improvements in screening procedures, many older adults at risk for malnutrition are not identified, which prevents effective management. Utilizing interdisciplinary approaches toward malnutrition screening is both effective and feasible. Physical therapists can play an important role in both the identification and management of malnutrition in older adults by remaining aware of common nutritional concerns in older adults and performing routine malnutrition screening.
Distinguishing Dementia With Lewy Bodies From Alzheimer Disease
Authors: Bregman Noa , Kavé Gitit , Mirelman Anat , Thaler Avner , Gana Weisz Mali , Bar-Shira Anat , Orr-Urtreger Avi , Giladi Nir , Shiner Tamara
Published: January 2019

Cognitive deficits beyond memory impairment, such as those affecting language production or executive functioning, can be useful in clinically distinguishing between dementia syndromes. We tested the hypothesis that Ashkenazi Jewish (AJ) patients who have dementia with Lewy bodies (DLB) and carry glucocerebrosidase (GBA) mutations will have verbal fluency deficits different from those found in Alzheimer disease (AD), whereas AJ patients with DLB who have no GBA mutations will have similar deficits in verbal fluency to those found in AD. We compared performance in phonemic and semantic verbal fluency tasks in 44 AJ patients with DLB and 20 patients with AD, matched for age, education, and age of immigration. All groups were found to have a deficit in semantic verbal fluency. On conducting the phonemic task, patients with DLB who carried GBA mutations scored more poorly than patients with AD, whereas DLB-noncarriers performed similarly to patients with AD. We suggest that verbal fluency tasks could serve as a possible clinical marker to subtype patients with DLB, with phonemic fluency being a marker for GBA-associated DLB.
Role of Cerebrospinal Fluid Biomarkers and (18)F-florbetapir PET Imaging in the Diagnosis of Primary Progressive Aphasia
Authors: Perini Giulia , Cotta Ramusino Matteo , Sinforiani Elena , Franciotta Diego , Trifirò Giusppe , Ceroni Mauro , Costa Alfredo
Published: January 2019

The use of biomarkers has recently supported the association between Alzheimer disease (AD) pathology and the logopenic variant of primary progressive aphasia (PPA). We aim to investigate possible differences in cerebrospinal fluid (CSF) biomarker concentrations in the three PPA variants, and to assess any agreement between CSF biomarkers and (18)F-florbetapir PET. A group of 10 PPA were retrospectively enrolled. Patients with logopenic variant (lvPPA) showed different levels of Aβ1-42 and p-tau compared to nonfluent/agrammatic and semantic variants (nfv/svPPA). All nfv/svPPA patients had negative amyloid PET. Among the lvPPA group, a negative amyloid PET was found only in one patient, who was also the only one to display a normal CSF. Thus, this small cohort appeared to display an excellent agreement between CSF and (18)F-florbetapir PET and suggest that these examinations may have the same validity in detecting in vivo evidence of AD pathology in PPA clinical variants.
Cholinesterase Inhibitors May Not Benefit Mild Cognitive Impairment and Mild Alzheimer Disease Dementia
Authors: Han Jee-young , Besser Lilah M. , Xiong Chengjie , Kukull Walter A. , Morris John C.
Published: January 2019

Introduction:

We investigated whether cholinesterase inhibitors (ChEIs) benefit cognitive outcomes in mild cognitive impairment due to Alzheimer disease (MCI-AD) and in mild AD dementia (ADdem).

Methods:

Data from 2242 individuals, clinically diagnosed with MCI-AD [Clinical Dementia Rating (CDR), 0 or 0.5] or with mild ADdem (CDR, 0.5 or 1), were available from the National Alzheimer’s Coordinating Center’s (NACC) Uniform Data Set (UDS). General linear mixed models were used to examine the annual change in the CDR Sum of Boxes (CDR-SB) and in neuropsychological performance. We compared slopes before and after ChEI initiation among ChEI users, and also compared the change in scores of ChEI users versus nonusers.

Results:

Thirty-four percent of 944 MCI-AD and 72% of 1298 ADdem participants were ChEI users. Cognitive decline was greater after ChEI initiation in MCI-AD and ADdem groups (eg, MCI-AD, CDR-SB: 0.03 points/y before initiation; 0.61 points/y after initiation, P<0.0001). Both MCI-AD and ADdem groups had faster decline after ChEI initiation than nonusers (eg, MCI-AD, CDR-SB: 0.61 points/y, ChEI users; 0.24 points/y, nonusers, P<0.0001).

Discussion:

This study suggests that ChEI use may not improve the cognitive course in MCI-AD and mild ADdem.
LAmbDA: Label Ambiguous Domain Adaption Dataset Integration Reduces Batch Effects and Improves Subtype Detection
Authors: Johnson Travis S , Huang Zhi , Yu Christina Y , Wang Tongxin , Wu Yi , Han Yatong , Hung Kun , Zhang Jie
Published: January 2019

Motivation

Rapid advances in single cell RNA sequencing have produced more granular subtypes of cells in multiple tissues from different species. There exists a need to develop rigorous methods that can i) model multiple datasets with ambiguous labels across species and studies and ii) remove systematic biases across datasets and species.

Results

We developed a species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets and applied our framework on scRNA-seq experiments. These models mapped corresponding cell types between datasets with inconsistent labels while simultaneously reducing batch effects. We achieved high accuracy in labeling cellular subtypes (weighted accuracy pancreas: 91%, brain: 78%) using LAmbDA Random Forest. LAmbDA Feedforward 1 Layer Neural Network achieved higher weighted accuracy in labeling cellular subtypes than CaSTLe or MetaNeighbor in brain (48%, 32%, 20% respectively). Furthermore, LAmbDA Feedforward 1 Layer Neural Network was the only method to correctly predict ambiguous cellular subtype labels in both pancreas and brain compared to CaSTLe and MetaNeighbor. LAmbDA is model- and dataset-independent and generalizable to diverse data types representing an advance in biocomputing.

Availability:github.com/tsteelejohnson91/LAmbDA

Contact:kunhuang@iu.edu,jizhan@iu.edu
Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells
Authors: Rooijers Koos , Markodimitraki Corina M. , Rang Franka J. , Vries Sandra S. de , Chialastri Alex , Luca Kim de , Mooijman Dylan , Dey Siddharth S. , Kind Jop
Published: January 2019

The epigenome plays a critical role in regulating gene expression in mammalian cells. However, understanding how cell-to-cell heterogeneity in the epigenome influences gene expression variability remains a major challenge. Here we report a novel method for simultaneous single-cell quantification of protein-DNA contacts with DamID and transcriptomics (scDamID&T). This method enables quantifying the impact of protein-DNA contacts on gene expression from the same cell. By profiling lamina-associated domains (LADs) in human cells, we reveal different dependencies between genome-nuclear lamina (NL) association and gene expression in single cells. In addition, we introduce the E. coli methyltransferase, Dam, as an in vivo marker of chromatin accessibility in single cells and show that scDamID&T can be utilized as a general technology to identify cell types in silico while simultaneously determining the underlying gene-regulatory landscape. With this strategy the effect of chromatin states, transcription factor binding, and genome organization on the acquisition of cell-type specific transcriptional programs can be quantified.
VSIM: Visualization and simulation of variants in personal genomes with an application to premarital testing
Authors: Althagafi Azza , Hoehndorf Robert
Published: January 2019

Background

Interpretation of personal genomics data, for example in genetic counseling, is challenging due to the complexity of the data and the amount of background knowledge required for its interpretation. This background knowledge is distributed across several databases. Further information about genomic features can also be predicted through machine learning methods. Making this information accessible more easily has the potential to improve interpretation of variants in personal genomes.

Results

We have developed VSIM, a web application for the interpretation and visualization of variants in personal genome sequences. VSIM identifies disease variants related to Mendelian, complex, and digenic disease as well as pharmacogenomic variants in personal genomes and visualizes them using a webserver. VSIM can further be used to simulate populations of children based on two parent genomes, and can be applied to support premarital genetic counseling. We make VSIM available as source code as well as through a container that can be installed easily in network environments in which genomic data is specially protected. VSIM and related documentation is freely available athttps://github.com/bio-ontology-research-group/VSIM.

Conclusions

VSIM is a software that provides a web-based interface to variant interpretation in genetic counseling. VSIM can also be used for premarital genetic screening by simulating a population of children and analyze the disorder they might be carrying.
tealeaves: an R package for modelling leaf temperature using energy budgets
Authors: Muir Christopher. D.
Published: January 2019

Plants must regulate leaf temperature to optimize photosynthesis, control water loss, and prevent damage caused by overheating or freezing. Physical models of leaf energy budgets calculate the energy fluxes and leaf temperatures for given a set leaf and environmental parameters. These models can provide deep insight into the variation in leaf form and function, but there are few computational tools available to use these models. Here I introduce a new R package calledtealeavesto make complex leaf energy budget models accessible to a broader array of plant scientists. This package enables novice users to start modelling leaf energy budgets quickly while allowing experts customize their parameter settings. The code is open source, freely available, and readily integrates with other R tools for scientific computing. This paper describes the current functionality oftealeaves, but new features will be added in future releases. This software tool will advance new research on leaf thermal physiology to advance our understanding of basic and applied plant science.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Authors: Meijenfeldt F.A. Bastiaan von , Arkhipova Ksenia , Cambuy Diego D. , Coutinho Felipe H. , Dutilh Bas E.
Published: January 2019

Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high-quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. In a real-world challenge, we apply BAT to over 900 MAGs from a recent rumen metagenomics study and classified 97% consistently with prior phylogeny-based classifications, but in a fully automated fashion.
Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
Authors: Daughtry Brittany L. , Rosenkrantz Jimi L. , Lazar Nathan H. , Fei Suzanne S. , Redmayne Nash , Torkenczy Kristof A. , Adey Andrew , Yan Melissa , Gao Lina , Park Byung , Nevonen Kimberly A. , Carbone Lucia , Chavez Shawn L.
Published: January 2019

Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously showed that human preimplantation embryos encapsulate missegregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N = 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping showed that these chromosome-containing cellular fragments (CCFs) can be maternally or paternally derived and display double-stranded DNA breaks. DNA breakage was further indicated by reciprocal subchromosomal losses/gains between blastomeres and large segmental errors primarily detected at the terminal ends of chromosomes. By combining time-lapse imaging with scDNA-seq, we determined that multipolar divisions at the zygote or two-cell stage were associated with CCFs and generated a random mixture of chromosomally normal and abnormal blastomeres with uniparental or biparental origins. Despite frequent chromosome missegregation at the cleavage-stage, we show that CCFs and nondividing aneuploid blastomeres showing extensive DNA damage are prevented from incorporation into blastocysts. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination via cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination
Authors: Ocampo Josefina , Chereji Răzvan V. , Eriksson Peter R. , Clark David J.
Published: January 2019

Most yeast genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. We have examined the interplay between RSC (a conserved essential SWI/SNF-type complex that determines NDR size) and the ISW1, CHD1, and ISW2 nucleosome spacing enzymes in chromatin organization and transcription, using isogenic strains lacking all combinations of these enzymes. The contributions of these remodelers to chromatin organization are largely combinatorial, distinct, and nonredundant, supporting a model in which the +1 nucleosome is positioned by RSC and then used as a reference nucleosome by the spacing enzymes. Defective chromatin organization correlates with altered RNA polymerase II (Pol II) distribution. RSC-depleted cells exhibit low levels of elongating Pol II and high levels of terminating Pol II, consistent with defects in both termination and initiation, suggesting that RSC facilitates both. Cells lacking both ISW1 and CHD1 show the opposite Pol II distribution, suggesting elongation and termination defects. These cells have extremely disrupted chromatin, with high levels of closely packed dinucleosomes involving the second (+2) nucleosome. We propose that ISW1 and CHD1 facilitate Pol II elongation by separating closely packed nucleosomes.
Referees’ Attitudes toward Open Peer Review and Electronic Transmission of Papers
Authors: Melero R. , López-Santoveña F.
Published: January 2019

A survey was mailed to 293 referees from the review board of Food Science and Technology International with the following personal characteristics: ages: 35–45 (35%), 45–55 (37%), and 55–65 (27%); 93% PhD graduates; 69% male, 98% researchers, 82% teachers too, 85% review for other journals as well to assess reviewers’ attitudes or preferences in favor of or against masking their identity, and toward the electronic transmission of papers for review. The reviewers were mainly from Europe, North America, and South America. The questionnaire was anonymous and asked if respondents were in favor of an open review or masking of the reviewers, and if they agreed with the electronic transmission of the papers for their review (both from the point of view of author and reviewer). The response rate was 35% (103 respondents). The consistency between the answers as being authors or reviewers when asked by the peer review process was significant ( P<0.001) without significant differences in terms of gender or age. Seventy-five percent were in favor of masking reviewers, and 17% completely favored unblinded review. The consistency between the answers for paper transmission was significant ( P<0.001) without significant differences in terms of gender or age. Seventy-five percent were in favor of electronic transmission, 25% were against it. There was a significant association between the answers in favor of or against e-transmission and the age either as reviewers ( P=0.009) or as authors ( P= 0.031). The other associations between the system of review and gender or age were not significant. There was a preference among the participants for masking the reviewers, and a tendency to use the Web as the transmission medium because it is considered faster, easier, simpler, and more economic.
Lipid Binding of Fresh and Stored Formulated Wheat Breads. Relationships with Dough and Bread Technological Performance
Authors: Collar C. , Martínez J. C. , Rosell C. M.
Published: January 2019

Lipid binding in fresh and stored soured started breads formulated with nonfat [sodium carboxymethylcellulose (CMC), hydroxypropylmethylcellulose (HPMC), fungal α-amylase-and fat–monoglycerides (MGL), diacetyl tartaric acid ester of mono-diglycerides (DATEM) and sodium stearoyl lactylate (SSL)] additives were determined. Results were correlated with dough and bread technological performance during breadmaking and storage. A preferential binding of the added SSL to the starch with a concomitant displacement of endogenous polar lipids from starch to gluten was observed. Monoglycerides partly bound to the starch and partial remained in the pool of free lipids with displacement of endogenous polar lipids from gluten to starch and free fractions. Addition of DATEM induced similar changes as SSL in association pattern and as MGL in polar lipid translocation. Hydrocolloids showed preferential bindings to the gluten (CMC) and to the starch (HPMC) respectively, associated to a significant displacement of endogenous neutral gluten-bounded lipids to the starchy fraction (CMC) and to a significant release of both starch- and gluten-bonded lipids (HPMC). Addition of α-amylase promoted both a release of endogenous bonded lipids and a binding of glycolipids to the starch whereas the sourer starter induced disaggregation of the starch– and gluten–lipid complexes. Suitable trends in bread lipid parameters for high fermentative power, delayed starch gelatinization, edible fresh bread and reduced bread staleness corresponded to high values of neutral lipids of bonded fractions and high total glycolipid content achieved by the incorporation of SSL and/or CMC into dough formulation.
Long Term Osmotic Dehydration Processes of Orange Peel at Atmospheric Pressure and by Applying a Vacuum Pulse
Authors: Cháfer M. , González-Martínez C. , Ortolá M. D. , Chiralt A.
Published: January 2019

Osmotic dehydration is a useful tool to obtain orange peel products with good sensory acceptance and stability. Osmodehydration of orange peel has been carried out in different osmotic solutions (65 Brix sucrose, 55 Brix glucose and concentrated rectified grape must) at 40 and 50 C for different durations (0–10 days), at atmospheric pressure and by applying a vacuum pulse at the beginning of the process. Changes in sample composition (water and soluble solid contents), weight, volume, density and porosity were analyzed. In all conditions, samples reached the same sample solute content as the osmotic solution at about 24 h of treatment, and the concentration rate was faster when vacuum pulse was applied. Mass transfer behavior showed that impregnation of the peel pores occurred to a great extent, not only when applying vacuum pulse, but also in treatments at normal pressure, due to the capillary effects and pressure gradients generated in the tissue associated with structural changes. Impregnation contributed to compositional changes and weight development of the sample. The greater the osmotic solution viscosity, the lower the impregnation level at equilibrium, which was always promoted by vacuum pulse.
Microstructure Changes During the Xixona Turrón Manufacture Analyzed by Light Microscopy
Authors: Perez-Munuera I. , Lewis D. F. , Lluch M. A.
Published: January 2019

Xixona turrón [Xixona nougat] is a typical Spanish confectionery product made still according to the traditional craft method. This work analyzed the microstructural changes during Xixona turrón manufacture by light microscopy. Different sample preparation methods provided useful complementary information for the understanding of the Xixona turrón structure. A progressively closer contact between a ‘‘sugar phase’’ and a ‘‘fat phase’’ is observed during processing. Inside these phases were immersed many protein bodies and a lot of cellular debris from almond tissue. At the initial stages of mixing the toasted almond paste with the sugar and honey mass, the lipid and sugar phases were relatively discrete. However, as the process developed, the relatively large aerated sugar particles, and to some extent the almond cell debris and protein bodies, were trapped within the lipid phase. In the step when the paste is heated at 65°C, gently stirred, the sugar and plant cell wall material tended to become more finely dispersed. The finished product seemed to consist of twin continuous phases in which the sugar, plant cell wall and protein bodies have formed a ‘‘sugar phase’’ that is infiltrated by the lipid fraction or ‘‘fat phase’’. This structure could contribute to the relatively ‘‘crispy’’ texture of Xixona turrón although the ‘‘oily’’ feel of the product clearly stated that the lipid phase was not extensively encapsulated in the product.
Design, 3D printing and validation of a novel low-cost high-capacity sitting-drop bridge for protein crystallization
Authors: Talapatra Sandeep K. , Penny Matthew R. , Hilton Stephen T. , Kozielski Frank
Published: January 2019

Sitting-drop protein crystallization is not used as commonly as the hanging-drop method for crystal optimization owing to the limitations of commercially available sitting-drop bridges, particularly when they are used in conjunction with 24-well crystallization plates. The commercially available sitting-drop bridge, containing space for only a single drop, restricts their wider use. Proteins that preferentially crystallize under sitting-drop conditions therefore require more work, time and resources for their optimization. In response to these limitations, and using 3D printing, a new sitting-drop bridge has been designed and developed, where five crystallization drops can be placed simultaneously in each well of a 24-well crystallization plate. This significantly simplifies the process and increases the potential of sitting drops in crystal optimization, reducing costs and hence overcoming the limitations of current approaches.
Fast positioning for X-ray scanning microscopy by a combined motion of sample and beam-defining optics
Authors: Odstrcil Michal , Lebugle Maxime , Lachat Thierry , Raabe Jörg , Holler Mirko
Published: January 2019

Scanning X-ray microscopy such as X-ray ptychography requires accurate and fast positioning of samples in the X-ray beam. Sample stages often have a high mobile mass as they may carry additional mechanics or mirrors for position measurements. The high mobile mass of a piezo stage can introduce vibrations in the setup that will lead to imaging quality deterioration. Sample stages also require a large travel range which results in a slow positioning step response and thus high positioning overhead. Moving lightweight X-ray optics, such as focusing Fresnel zone plates, instead of the sample can improve the situation but it may lead to undesired variations in the illumination probe which may result in reconstruction artifacts. This paper presents a combined approach in which a slow sample stage mechanism covers the long distance range for a large field of view, and a light-weight optics scanner with a small travel range creates a superimposed motion to achieve a fast step response. The step response in the ptychographic tomography instrument used was thereby improved by an order of magnitude, allowing for efficient measurement without loss of imaging quality.
Elite status talks, but how loudly and why? Exploring elite CSR micro-politics
Authors: Heath Robert L. , Waymer Damion
Published: January 2019

Purpose

The purpose of this paper is to investigate the proactive role elite organizations play within-network corporate social responsibility (CSR) performance by determining whether organizations can be identified that serve as aspirational CSR role models. The assumption is that elite CSR performance inspires and challenges other in-network actors to raise their standards in order to be legitimate, and resource rewardable.

Design/methodology/approach

Three cases are discussed to exemplify elite CSR: historical: recognizing the value of embracing a trend in improved standards of meatpacking, Armour Meatpacking campaigned for sanitary meatpacking and implemented strategic change; global energy: Chevron Corporation conducts “business in a socially and environmentally responsible manner, respecting the law and universal human rights to benefit the communities where we work”; and non-profit: “Elite” universities’ CSR standards attract bright faculty and students and build beneficial relationships with industry, government and peers.

Findings

Elite institutions raise CSR standards by using issue trends to guide strategic change that can performatively demonstrate the societal value of proactive leadership that elevates standards and increases the reward value to communities and organizations that is achieved by adopting higher standards.

Research limitations/implications

Through micro-politics that increase CSR social productivity, elite CSR standards earn rewards for exemplary organizations and subsequently raise standards for in-network organizations to, in turn, achieve the license to operate.

Practical implications

Discussions of CSR should consider the influences that establish CSR standards. To that end, this paper offers the explanatory power of a micro-political, societal productivity approach to CSR based on the pragmatic/moral resource dependency paradigm.

Social implications

The paper reasons that higher CSR standards result when NGO stakeholder critics and/or government agencies exert micro-political pressure. In response to such pressure, elite organizations, those that are or can meet those higher CSR standards, proactively demonstrate how higher CSR standards can accrue resources that benefit them and society. Elite CSR performance challenges other in-network actors to raise standards in order to be legitimate, that is resource rewardable.

Originality/value

Because elite organizations understand the reward advantage of higher levels of CSR, they proactively elevate the discuss of standards and advantages for achieving them, and penalties for falling short.