Testing Gene-Gene Interactions Based on a Neighborhood Perspective in Genome-wide Association Studies

Unexplained genetic variation that causes complex diseases is often induced by gene-gene interactions (GGIs). Gene-based methods are one of the current statistical methodologies for discovering GGIs in case-control genome-wide association studies that are not only powerful statistically, but also interpretable biologically. However, most approaches include assumptions about the form of GGIs, which results in poor statistical performance. As a result, we propose gene-based testing based on the maximal neighborhood coefficient (MNC) called gene-based gene-gene interaction through a maximal neighborhood coefficient (GBMNC). MNC is a metric for capturing a wide range of relationships between two random vectors with arbitrary, but not necessarily equal, dimensions. We established a statistic that leverages the difference in MNC in case and in control samples as an indication of the existence of GGIs, based on the assumption that the joint distribution of two genes in cases and controls should not be substantially different if there is no interaction between them. We then used a permutation-based statistical test to evaluate this statistic and calculate a statistical p-value to represent the significance of the interaction. Experimental results using both simulation and real data showed that our approach outperformed earlier methods for detecting GGIs.</jats:p

Dysbiosis of human gut microbiome in young-onset colorectal cancer

AbstractThe incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 310 samples is used to validate the results. Furthermore, species-level and functional analysis are performed by metagenome sequencing using 200 samples. Gut microbial diversity is increased in yCRC. Flavonifractor plautii is an important bacterial species in yCRC, while genus Streptococcus contains the key phylotype in the old-onset colorectal cancer. Functional analysis reveals that yCRC has unique characteristics of bacterial metabolism characterized by the dominance of DNA binding and RNA-dependent DNA biosynthetic process. The random forest classifier model achieves a powerful classification potential. This study highlights the potential of the gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with yCRC.</jats:p

Electronic structure and dynamic properties of two-dimensional W x Mo 1? : x S 2 ternary alloys from first -principles calculations

Two-dimensional transition metal dichalcogenide materials are of great interest for the development of semiconductor devices because of their diverse properties. In this paper, we discovered the ground states of WxMo1−xS2 alloys and discussed their electronic structures and phonon properties in detail by the cluster expansion method and the first principle calculation. Three ground-state structures of WxMo1−xS2 alloys, W1/3Mo2/3S2, W1/2Mo1/2S2, and W2/3Mo1/3S2, have low order–disorder phase transition temperatures, T1/3 = 102.3 K, T1/2 = 87.8 K, and T2/3 = 102.2 K, estimated by mean field theory. Their bandgaps exhibit a nonlinear increase with increasing W content. All ground structures are dynamically stable without imagine frequency in phonon dispersion. W doping into single layer MoS2 leads low frequency optical modes hybriding with acoustic modes and lowering down the low frequency band due to larger mass of W atoms. All these may improve the developments of WxMo1−xS2 alloys devices.</p

Clinical diagnosis and treatment of common respiratory tract infections in relation to microbiological profiles in rural health facilities in China: implications for antibiotic stewardship

AbstractBackgroundThis paper tries to describe prevalence and patterns of antibiotics prescription and bacteria detection and sensitivity to antibiotics in rural China and implications for future antibiotic stewardship.MethodsThe study was implemented in one village clinic and one township health center in each of four rural residential areas in Anhui Province, China. It used mixed-methods comprising non-participative observations, exit-survey and microbiological study. Observations were conducted to record clinical diagnosis and antibiotic prescription. Semi-structured questionnaire survey was used to collect patient’s sociodemographic information and symptoms. Sputum and throat swabs were collected for bacterial culture and susceptibility testing.ResultsA total of 1068 (51.0% male vs 49.0% female) patients completed the study with diagnosis of respiratory tract infection (326,30.5%), bronchitis/tracheitis (249,23.3%), pharyngitis (119,11.1%) and others (374, 35.0%). They provided 683 sputum and 385 throat swab specimens. Antibiotics were prescribed for 88% of the RTI patients. Of all the specimens tested, 329 (31%) were isolated with bacteria. The most frequently detected bacteria wereK. pneumonia(24% in all specimens),H. influenza(16%),H. parainfluenzae(15%),P. aeruginosa(6%),S.aureus(5%),M. catarrhalis(3%) andS. pneumoniae(2%).ConclusionsThe study establishes the feasibility of conducting microbiological testing outside Tier 2 and 3 hospitals in rural China. It reveals that prescription of antibiotics, especially broad-spectrum and combined antibiotics, is still very common and there is a clear need for stewardship programs aimed at both reducing the number of prescriptions and promoting single and narrow-spectrum antibiotics.</jats:sec

Alternations of Blood Pressure Following Surgical or Drug Therapy for Prolactinomas

Several subtypes of pituitary neuroendocrine tumors (PitNETs), such as acromegaly and Cushing&rsquo;s disease, can result in hypertension. However, whether prolactinoma is associated with this complication remains unknown. Moreover, the effect of treatment with surgery or drugs on blood pressure (BP) is unknown. Herein, a retrospective study reviewed 162 patients with prolactinoma who underwent transsphenoidal surgery between January 2005 and December 2022. BP measurements were performed 1 day before and 5 days after surgery. Accordingly, patients&rsquo; medical characteristics were recorded. In addition, in situ rat and xenograft nude-mice prolactinoma models have been used to mimic prolactinoma. In vivo BP and serum prolactin (PRL) levels were measured after cabergoline (CAB) administration in both rats and mice. Our data suggest that surgery can effectively decrease BP in prolactinoma patients with or without hypertension. The BP-lowering effect was significantly associated with several variables, including age, sex, disease duration, tumor size, invasion, dopamine agonists (DAs)-resistance, recurrence, and preoperative PRL levels. Moreover, in situ and xenograft prolactinomas induced BP elevation, which was alleviated by CAB treatment without and with a statistical difference in rats and mice, respectively. Thus, surgery or CAB can decrease BP in prolactinoma, indicating that pre- and postoperative BP management becomes essential

Is hepatitis E virus an emerging problem in industrialized countries?

Hepatitis E virus (HEV) is yearly responsible for approximately 20 million infections worldwide. Although most infections occur in developing countries, HEV appears to be an emerging problem in several industrialized countries, where it is mostly associated with either traveling to an HEV endemic area or contact with pigs, which represent a major reservoir of HEV. The major risk groups for HEV infection and its ensuing complications are elderly men, pregnant women, young children, immunocompromised patients, patients with preexisting liver disease, and workers that come into close contact with HEV-infected animals. Whereas HEV mainly causes acute self-limiting infections, chronic infections may occur among immunocompromised patients (e.g., transplant recipients and human immunodeficiency virus [HIV]-infected patients). Accordingly, HEV-HIV coinfection leads to accelerated liver cirrhosis and increased mortality rates compared to HEV infection alone, which is, except during pregnancy, usually associated with only low mortality. In the Western world, the most common genotype (gt) causing HEV infection is gt 3. Ribavirin (RBV) and interferon have been used successfully for treatment of HEV, but this treatment is contraindicated in certain patient groups. Therefore, novel antiviral compounds are highly needed, especially given that viral isolates with RBV resistance have been recently identified. Moreover, eradication of HEV is hampered by long-term environmental persistence of the virus, which represents a continuous source of the virus. In 2011, the first prophylactic HEV vaccine, Hecolin, was approved in China, but it is not yet globally available. In this review, we will discuss the molecular virology of HEV, mode of transmission in industrialized countries, and potential implications for different specific patient populations