bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between ERAP1 polymorphisms and susceptibility to ankylosing spondylitis
Authors: Jiang Yuqing , Ren Yi , Zhou Dong , Xu Youjia 
Published: November 2018

Abstract

Background:
The genetic factor is importantly enrolled in the pathogenesis of ankylosing spondylitis (AS) and haplotype leukocyte antigen (HLA)-B27 is the most well-known. However, only 1% to 5% of B27-positive individuals will develop AS, and it confers only 20% to 30% of the overall genetic risks, indicating more genes other than HLA-B27 may play important roles in AS pathologies. The present study aims to investigate whether the polymorphisms of endoplasmic reticulum aminopeptidase 1 (ERAP1) is associated with increased risk of AS susceptibility.

Methods:
The Cochrane library, Pubmed, and Embase databases were carefully searched for potential researches published before May 30, 2018. The title, abstract, and full text were assessed to determine whether the paper was suitable for inclusion. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were presented to assess the associations between ERAP1 polymorphisms and AS susceptibility.

Results:
The study finally enrolled 10 papers, 4 matched single nucleotide polymorphisms (SNPs) of ERAP1 (rs27044, rs27434, rs30187, and rs27037), and a total of 30552 patients (12492 with AS and 18060 for control). No significant difference was found between the AS susceptibility and polymorphisms of rs27044 and rs27434. However, there was a significant association between ERAP1 polymorphisms rs30187 and rs27037 (T vs C, OR, 1.322, 95% CI = 1.240–10410, P <.05; T vs G, OR, 1.247, 95% CI = 1.149–1.353; P <.05; respectively) and AS susceptibility.

Conclusion:
There was a significant association between ERAP1 polymorphisms (rs30187 and rs27037) and increased risk of AS susceptibility.
Suspended over length biliary stents versus conventional plastic biliary stents for the treatment of biliary stricture
Authors: Yan Xiue , Huang Yonghui , Chang Hong , Zhang Yaopeng , Yao Wei , Li Ke 
Published: November 2018

Abstract
To compare patency between suspended over length biliary stents (SOBSs; made from nasobiliary tube) and conventional plastic biliary stents (CPBSs).
We retrospectively analyzed 61 patients with extrahepatic biliary stricture who underwent SOBS placement (intrahepatic bile duct) and 74 patients who underwent CPBS placement. Stent patency and complications were compared.
The SOBS group was slightly older and contained more females than the CPBS group but other baseline characteristics were similar. Malignant biliary obstruction accounted for 57.4% (SOBS group) and 45.9% (CPBS group) of cases. Technical success rate, hospital stay and post-procedure complications were similar between groups. Median patency in the CPBS and SOBS group was 116 (2–360) days and 175 (3–480) days, respectively (P <.001). The SOBS group had lower stent occlusion rates than the CPBS group at 3 months (9.8% vs 36.5%), 4 months (22.0% vs 55.4%), 5 months (35.6% vs 67.6%), and 6 months (39.3% vs 77.0%) (all P <.01). In Cox regression analysis, stent type (SOBS vs CPBS) was the only factor associated with patency (hazard ratio [HR]: 3.449; 95% CI: 1.973-6.028; P <.001).
SOBS may have better medium-term patency than CPBS for benign/malignant biliary stricture.
Radiofrequency ablation in a patient with radiation enteritis
Authors: Shen Xing-jie , Liu Liang , Zhu Jing-yu 
Published: November 2018

Abstract

Rationale:
Radiation enteritis (RE) is one of the serious complications caused by the radiotherapy and it can occur in any segment of the intestine, including small intestine, colon, and rectum. It can cause a number of serious problems of the intestine, such as chronic ulcers, bleeding, intestinal stenosis, intestinal fistula, and perforation. At present, there is no standard treatment guideline for the RE.

Patient Concerns:
A 54-year-old male patient received surgery and chemotherapy for rectal cancer and radiofrequency ablation (RFA) for a single metastatic carcinoma of the liver. Three years later, he was diagnosed with recurrent lesion in the rectal anastomotic stoma and was treated with radiotherapy with a total dose of 70 Gy. Following this, he had persistent abdominal pain and diarrhea for 1 year.

Diagnoses:
Colonoscopy confirmed a diagnosis of RE.

Interventions:
Since intestinal probiotics, intestinal mucosal protectants, antidiarrheal drugs, and other treatments were not effective; the patient was treated by RFA.

Outcomes:
Clinical symptoms of the patient were gradually decreased after the RFA. Colonoscopy examination was performed 3 months later and intestinal mucosa was found to have healed well.

Lessons:
RFA is an effective treatment for patients with RE, and it is expected to be one of the standard treatments for the RE.
Spontaneous adrenal hematoma in pregnancy
Authors: Yang Ling , Zhu Yu-Chun , Liu Rong-Bo 
Published: November 2018

Abstract

Rational:
Spontaneous adrenal hematoma in pregnancy is a very rare condition. Herein we present an additional rare case of unilateral spontaneous adrenal hematoma in a pregnant woman, aiming to share this experience and summarize the signal characteristics of simple adrenal hematoma in magnetic resonance imaging (MRI).

Patient concerns:
A 28-year old pregnant woman was referred to our hospital with a vague paroxysmal left-side back pain at 17 weeks of gestation.

Diagnosis:
MR scan of the abdomen revealed an 8.1 × 7.7 × 6.8 cm round mass in the left adrenal region, which showed a rim of acute hemorrhage signal. Due to the stable condition of the patient and fetus, she was admitted for observation. Repeat MR scan was performed a month later, and it showed a stable mass with marginal subacute bleeding signal.

Interventions:
Laparoscope excision of the hematoma was performed.

Outcomes:
Simple adrenal hematoma was confirmed by pathological examinations. And the patient was discharged 3 days later with normal renal and adrenal functions.

Lessons:
The most important characteristic of adrenal hematoma is the high-signal rim on T1-weighted MR images, and the clinicians should make individualized treatment plan for every patient encountered in the future who might have different clinical conditions.
Association between polymorphisms in estrogen metabolism genes and breast cancer development in Chinese women
Authors: Qiu Juanjuan , Du Zhenggui , Liu Jingping , Zhou Yi , Liang Faqing , Lü Qing 
Published: November 2018

Abstract
We comprehensively identified polymorphisms in estrogen-metabolizing genes that may be associated with breast cancer initiation in Chinese women, via an ongoing prospective case–control study.
An ongoing prospective case–control study of 427 female case patients diagnosed with breast cancer from August 2013 to March 2015 and 536 women (case controls) with no prior history of cancer or benign breast tumors was performed. Buccal cell specimens were obtained using the cotton swabbing method. DNA was extracted from the buccal cells using the phenol/chloroform method. Genotype was carried out for 5 single nucleotide polymorphisms (rs4646903, rs1056836, rs1695, rs4970737, and rs4680) using direct sequencing.
The polymorphic genotypes of glutathione S-transferase (GSTP1) (P = .044) and catechol-O-methyltransferase (COMT) (P = .008) showed significantly different distributions, while that of cytochrome P450 (CYP1B1) (P = .051) showed a slight difference in distribution between healthy women and patients with breast cancer. Individuals with homozygous variant genotypes for GSTP1 or COMT exhibited a higher risk of developing breast cancer than those with wild-type genotypes; however, for CYP1B1, the homozygous variant genotype was associated with a lower risk, and the heterozygous genotype for these 3 genes was not associated with breast cancer development.
An individual's risk of breast cancer is only influenced by the specific combination of risk-associated alleles of COMT and GSTP1, despite the protective effects of the homozygous CYP1B1 genotype revealed by univariate analysis.
Long-term follow-up after cure from chronic hepatitis C virus infection shows occult hepatitis and a risk of hepatocellular carcinoma in noncirrhotic patients
Authors: Lybeck Charlotte , Brenndörfer Erwin D. , Sällberg Matti , Montgomery Scott M. , Aleman Soo , Duberg Ann-Sofi 
Published: November 2018

Objectives
Curing of hepatitis C virus (HCV) infection primarily aims to prevent severe liver complications. Our objectives were to investigate the long-term presence and impact of occult HCV infection (OCI) and to study the outcomes in terms of liver disease after virological cure.

Patients and methods
A total of 97 patients with achieved sustained virological response (SVR) during 1990–2005 were followed either by a clinical follow-up (FU) visit with blood sampling and liver elastography (n=54) or through national registries for outcomes (n=43). To diagnose OCI among patients with SVR, a highly sensitive method was used to detect HCV-RNA traces in whole blood. The FU duration was a median of 10.5 years, with samples up to 21.5 years after the end of treatment (EOT).

Results
The majority of patients [52 (96%)] were HCV-RNA negative at FU, and regression of fibrosis was statistically significant. OCI was found in two (4%) of them at 8 and 9 years after EOT. These patients had F1 and F2 fibrosis before treatment and F2 at FU, but no other abnormal findings. Three previously noncirrhotic men were diagnosed with hepatocellular carcinoma 8–11 years after EOT.

Conclusion
Occult infection could be detected many years after the achievement of SVR but was not associated with serious liver disease. The majority had persistent viral eradication and regression of fibrosis after SVR. However, an increased risk of hepatocellular carcinoma may persist in the long term after SVR even in noncirrhotic patients. Further studies with FU after direct-acting antiviral therapy and on the long-term impact after cure are needed.
Intractable Central Pain in a Patient With Diffuse Glioma
Authors: Horan Nicholas Aaron , Pugh Terrence MacArthur 
Published: November 2018

Abstract
Central neuropathic pain can be difficult to treat and, subsequently, cause a great amount of disability and distress to patients, which limits quality of life. Common etiologies include the following: stroke, spinal cord injury, multiple sclerosis, infection, vasculitis, and malignancy. This case is a description of an 18-yr-old male patient diagnosed with a grade IV diffuse glioma who experienced severe neuropathic pain refractory to first-line treatment options including the following: gabapentinoids, tricyclic antidepressants, and selective serotonin and norepinephrine reuptake inhibitors. The patient remained on high-dose oral gabapentin as well as methadone and high-dose oxycodone for pain control at the time of submission. The aims of this case report were to review the nociceptive pathways and to explore the role of opioids in central neuropathic pain secondary to neoplasm because a better understanding of these topics can aid physiatrists in better taking care of these patients and improving function and quality of life.
Differentiating Transition Zone Cancers From Benign Prostatic Hyperplasia by Histogram Analysis of Apparent Diffusion Coefficient Maps With Standard and Ultrahigh b-value Diffusion-weighted MR Imaging
Authors: Lu Zhi-hua , Ji Li-biao , Zhao Wen-lu , Zhang Yong-sheng , Wu Jiang-fen , Li Xin , Shen Jun-kang 
Published: November 2018

Objective
To compare the diagnostic performance of standard and ultrahigh b-value Diffusion-weighted Imaging (DWI) using volumetric histogram analysis in differentiating transition zone (TZ) cancer from benign prostatic hyperplasia (BPH).

Methods
57 TZ cancer and 61 BPH patients received standard (1000 s/mm2) and ultrahigh b-value (2000 s/mm2) DWI. The diagnostic ability of ADC histogram parameters derived from two DWI for differentiating TZ cancer from BPH was determined by receiver operating characteristic curve.

Results
Median, minimum, the 10th, 25th percentile ADC in both ADC1000 and ADC2000 and skewness in ADC2000 had significant differences between TZ cancer and BPH (for all, P < 0.05).The 10th percentile ADC showed highest area under the ROC curve (AUC) in both ADC1000 and ADC2000.The 10th percentile ADC of ADC2000 showed significantly higher AUC than did ADC1000 (P = 0.0385).

Conclusions
The 10th percentile ADC obtained from ultrahigh b-value DWI performed better for differentiating TZ cancer from BPH.
CRISPR-based DNA and RNA detection with liquid-liquid phase separation
Authors: Spoelstra Willem Kasper , Jacques Jeroen M. , Nobrega Franklin L. , Haagsma Anna C. , Dogterom Marileen , Idema Timon , Brouns Stan J. J. , Reese Louis 
Published: November 2018

AbstractThe ability to detect specific nucleic acid sequences allows for a wide range of applications including identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence both enzymes activate a unique, indiscriminate nucleic acid cleavage activity, which has been exploited for detection of sequence specific nucleotides using labelled reporter molecules. We here present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Turbidity arises from coacervates of positively charged polyelectrolytes with long poly(dT) or poly(U) oligonucleotides. In the presence of a target sequence, long oligonucleotides are progressively shortened, changing the solution from turbid to transparent. We explain how oligonucleotide cleavage resolves LLPS by using a mathematical model which we validate with poly(dT) phase separation experiments. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.
In Silico Determined Properties of Designed Superoxide Dismutase-1 Mutants Predict ALS-like Phenotypes In Vitro and In Vivo
Authors: DuVal Michèle G. , McAlary Luke , Habibi Mona , Garg Pranav , Sher Mine , Cashman Neil R. , Allison W. Ted , Plotkin Steven S. 
Published: November 2018

AbstractThe underlying physical causes of SOD1-related ALS are still not well-understood. We address this problem here by computationally designing two de novo mutants, A89R and K128N, which were predicted theoretically to be either significantly destabilizing or stabilizing respectively. We subjected these in silico designed mutants to a series of experimental tests, including in vitro measures of thermodynamic stability, cell-based aggregation and toxicity assays, and an in vivo developmental model of zebrafish motor neuron axonopathy. The experimental tests validated the theoretical predictions: A89R is an unstable, highly-deleterious mutant, and K128N is a stable, non-toxic mutant. Moreover, K128N is predicted computationally to form an unusually stable heterodimer with the familial ALS mutant A4V. Consistent with this prediction, co-injection of K128N and A4V into zebrafish shows profound rescue of motor neuron pathology. The demonstrated success of these first principles calculations to predict the physical properties of SOD1 mutants holds promise for rationally designed therapies to counter the progression of ALS.SignificanceMutations in the protein superoxide dismutase cause ALS, and many of these mutants have decreased folding stability. We sought to pursue this thread using a synthetic biology approach, where we designed two de novo mutations, one stabilizing and one destabilizing, as predicted using computational molecular dynamics simulations. We then tested these mutants using in vitro, cell-based, and in vivo zebrafish models. We found that the unstable mutant was toxic, and induced a severe ALS phenotype in zebrafish; the predicted stable mutant, on the other hand, behaved even better than WT. In fact, it was able to rescue the ALS phenotype caused by mutant SOD1. We propose a mechanism for this rescue, which may provide an avenue for therapeutic intervention.
Multi-Scale Structural Analysis of Proteins by Deep Semantic Segmentation
Authors: Eguchi Raphael R. , Huang Po-Ssu 
Published: November 2018

AbstractRecent advancements in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds, and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation — a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structural quality assessment. We represent protein structures as 2D α-carbon distance matrices (“contact maps”), and train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model performs exceptionally well, achieving a per-residue accuracy of 90.8% on the test set (95.0% average accuracy over all classes; 87.8% average within-structure accuracy). The unique aspect of our classifier is that it encodes sequence agnostic residue environments from the PDB and can assess structural quality as quantitative probabilities. We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design.SignificanceRecent computational advances have allowed researchers to predict the structure of many proteins from their amino acid sequences, as well as designing new sequences that fold into predefined structures. However, these tasks are often challenging because they require selection of a small subset of promising structural models from a large pool of stochastically generated ones. Here, we describe a novel approach to protein model selection that uses 2D image classification techniques to evaluate 3D protein models. Our method can be used to select structures based on the fold that they adopt, and can also be used to identify regions of low structural quality. These capabilities yield a powerful tool for both protein design and structure prediction.
Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids
Authors: Houde Aimee Lee S. , Günther Oliver P. , Strohm Jeffrey , Ming Tobi J. , Li Shaorong , Kaukinen Karia H. , Patterson David A. , Farrell Anthony P. , Hinch Scott G. , Miller Kristina M. 
Published: November 2018

AbstractEarly marine survival of juvenile salmon is intimately associated with their physiological condition during ocean entry and especially smoltification. Smoltification is a developmental parr–smolt transformation allowing salmon to acquire the trait of seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+ATPase (NKA) activity or plasma hormones, but gill gene expression can be reliably used. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for Taq-Man qPCR assay design and their monthly expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon, and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport, and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness, and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt, and de-smolt trials from acute seawater transfers using a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt, or de-smolt.
Prediction in Human Auditory Cortex
Authors: Forseth KJ , Hickok G , Rollo Patrick , Tandon N 
Published: November 2018

AbstractSpoken language is thought to be facilitated by an ensemble of predictive mechanisms, yet the neurobiology of prediction for both speech perception and production remains unknown. We used intracranial recordings (31 patients, 6580 electrodes) from depth probes implanted along the anteroposterior extent of the supratemporal plane during rhythm listening, speech perception, and speech production. This revealed a frequency-multiplexed encoding of sublexical features during entrainment and a traveling wave of high-frequency activity across Heschl’s gyrus. Critically, we isolated two predictive mechanisms in early auditory cortex with distinct anatomical and functional characteristics. The first mechanism, localized to bilateral Heschl’s gyrus and indexed by low-frequency phase, predicts the timing of acoustic events (“when”). The second mechanism, localized to planum temporale in the language-dominant hemisphere and indexed by gamma power, predicts the acoustic consequence of speech motor plans (“what”). This work grounds cognitive models of speech perception and production in human neurobiology, illuminating the fundamental acoustic infrastructure – both architecture and function – for spoken language.