bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced immune responses, PI3K/AKT and JAK/STAT signaling pathways following hepatitis C virus eradication by direct-acting antiviral therapy among Egyptian patients: a case control study
Authors: Ramadan Haidi Karam-Allah , Badr Gamal , Ramadan Nancy K , Sayed Aml 
Published: January 2021

ABSTRACT
The use of direct-acting antivirals (DAAs) therapy for the treatment of hepatitis C virus (HCV) results in a high-sustained virological response (SVR) and subsequently alters liver immunologic environment. However, hepatocellular carcinoma (HCC) may occur after DAAs treatment. We aimed to clarify changes of immune responses, PI3K/AKT and JAK/STAT signaling pathways in HCV-induced liver diseases and HCC following DAAs treatment. Four cohorts were classified as chronic HCV patients, HCV-related cirrhosis without HCC, HCV-related cirrhosis and HCC, and healthy control group. The patient groups were further divided into treated or untreated with DAAs with SVR12. Increased percentages of CD3, CD8 and CD4, decreased CD4/FoxP3/CD25, CD8/PD-1 and CD19/PDL-1 were found in DAAs-treated patients in the three HCV groups. Following DAAs therapy, the levels of ROS, IL-1β, IL-6, IL-8 and TNF-α were significantly decreased in the three HCV groups. Treated HCV patients showed up regulation of p-AKT and p-STAT5 and down regulation of p-STAT3, HIF-1α and COX-2. In conclusion, DAAs enhance the immune response in chronic HCV and liver cirrhosis, hence our study is the first to show change in PI3K/AKT and JAK/STAT signaling pathways in different HCV-induced liver diseases after DAAs. In chronic HCV, DAAs have better impact on the immune response while in liver cirrhosis not all immune changes were prominent.
Elite Change and the Inception, Duration, and Demise of the Turkish–Israeli Alliance
Authors: Aydinli Ersel , Erpul Onur 
Published: January 2021

AbstractThis article investigates the emergence and puzzling termination of the Turkish–Israeli alliance (1996–2011). While a litany of studies has offered changing material circumstances, the conservative agenda of Turkey's AKP government, and other exogenous factors as possible explanations, these fail to capture the complexity of the situation. Instead, this article applies a modified neoclassical realist framework of analysis that longitudinally recontextualizes the alliance. Specifically, in both its inception and collapse, Turkey's elite decision-makers faced no apparent external threats and were free to pursue their favored foreign policy. Domestically, however, Turkey's elite structure was decisive. In the 1990s, the old elite used their institutional power to restrain emerging elites and used their alliance with Israel as a pretext to do so. A decade later, a new elite seized institutional power. No longer restrained domestically, and absent external enemies, the new elites targeted Israel as a menace to win further domestic support, but this eventuated in a series of events that led to the termination of the alliance. Overall, the article concludes that alliance policy can become erratic at the intersection of permissive international environments and elite-induced domestic conflicts.
Adventures of a Mathematician in Evolutionary Biology
Authors: Li Wen-Hsiung 
Published: January 2021

Foreword
In an occasional series of articles, we will be publishing autobiographical sketches from some of those working in the field of genome evolution. The series will feature both the very eminent, but also researchers closer to their start of their career, and those from underrepresented groups. The series will show the unusual paths that academics sometimes take and the obstacles they have overcome. We start this series with one of the most influential researchers in the field of molecular evolution, Wen-Hsiung Li. Wen-Hsiung has contributed enormously to the field and published on a wide diversity of topics, as described in this autobiographical sketch; he also wrote two textbooks, one of them with Dan Graur, which for many years were the bibles of the field. He was awarded the Motoo Kimura prize by the Society of Molecular Biology and Evolution in 2019 in recognition of his contributions to our subject.
Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish
Authors: Papetti Chiara , Babbucci Massimiliano , Dettai Agnes , Basso Andrea , Lucassen Magnus , Harms Lars , Bonillo Celine , Heindler Franz Maximilian , Patarnello Tomaso , Negrisolo Enrico 
Published: January 2021

AbstractThe vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
Metabolic Alteration in Plasma and Biopsies From Patients With IBD
Authors: Santoru Maria Laura , Piras Cristina , Murgia Federica , Leoni Vera Piera , Spada Martina , Murgia Antonio , Liggi Sonia , Lai Maria Antonia , Usai Paolo , Caboni Pierluigi , Manzin Aldo , Atzori Luigi 
Published: January 2021

AbstractBackgroundInflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract, with periods of latency alternating with phases of exacerbation, and include 2 forms: Crohn disease (CD) and ulcerative colitis (UC). Although the etiology of IBD is still unclear, the identification and understanding of pathophysiological mechanisms underlying IBD could reveal newly targeted intestinal alterations and determine therapeutic approaches.MethodsIn this study, by using gas chromatography-mass spectrometry, we characterized plasma and biopsies from the metabolomics profiles of patients with IBD compared with those of a control group.ResultsThe results showed a different metabolomics profile between patients with CD (n = 50) and patients with UC (n = 82) compared with the control group (n = 51). Multivariate statistical analysis of the identified metabolites in CD and UC showed changes in energetic metabolism, and lactic acid and ornithine in particular were altered in both plasma and colon biopsies. Moreover, metabolic changes were evidenced between the normal ileum and colon tissues. These differences disappeared when we compared the inflamed ileum and colon tissues, suggesting a common metabolism.ConclusionsThis study showed how the metabolomics profile could be a potential tool to identify intestinal alterations associated with IBD and may have application in precision medicine and for better defining the pathogenesis of the disease.
High-Containment Agriculture Animal Research: An AAALAC International Perspective
Authors: Harper Susan B , Bayne Kathryn , Anderson Kenneth E 
Published: January 2021

Abstract
Institutions that conduct high-containment agricultural research involving domestic livestock represent a specialized category of programs that are accredited by AAALAC International. The accreditation process includes a comprehensive assessment of the overall program of animal care and use. However, the complex design of these facilities and the unique care required for animals in this type of environment often mean that additional attention will be directed at areas regarded as higher risk when the programs are evaluated. Specific issues that may stimulate additional discussion and interest include animal housing practices, environmental conditions inside the facility, maintenance of procedure and support areas, methods for obtaining and safely transporting healthy research animals, strategies to minimize animal pain and distress, unusual protocol review challenges, and institutional policies relevant to personnel training and safety. These issues are further discussed to inform institutions of potential concerns that should be reviewed and assessed during internal preparations for accreditation visits by AAALAC site visit teams.
Efficacy of a novel lantibiotic, CMB001, against MRSA
Authors: Karczewski Jerzy , Brown Christine M , Maezato Yukari , Krasucki Stephen P , Streatfield Stephen J 
Published: January 2021

Abstract

Objectives
To evaluate the efficacy of a novel lantibiotic, CMB001, against MRSA biofilms in vitro and in an in vivo experimental model of bacterial infection.

Methods
Antibacterial activity of CMB001 was measured in vitro after its exposure to whole blood or to platelet-poor plasma. In vitro efficacy of CMB001 against a Staphylococcus aureus biofilm was studied using scanning electron microscopy. The maximum tolerable dose in mice was determined and a preliminary pharmacokinetic analysis for CMB001 was performed in mice. In vivo efficacy was evaluated in a neutropenic mouse thigh model of infection.

Results
CMB001 maintained its antibacterial activity in the presence of blood or plasma for up to 24 h at 37°C. CMB001 efficiently killed S. aureus within the biofilm by causing significant damage to the bacterial cell wall. The maximum tolerable dose in mice was established to be 10 mg/kg and could be increased to 30 mg/kg in mice pretreated with antihistamines. In neutropenic mice infected with MRSA, treatment with CMB001 reduced the bacterial burden with an efficacy equivalent to that of vancomycin.

Conclusions
CMB001 offers potential as an alternative treatment option to combat MRSA. It will be of interest to evaluate the in vivo efficacy of CMB001 against infections caused by other pathogens, including Clostridioides difficile and Acinetobacter baumannii, and to expand its pharmacokinetic/pharmacodynamic parameters and safety profile.
Effects of dietary iron level on growth performance, hematological status, and intestinal function in growing-finishing pigs
Authors: Deng Qingqing , Wang Yancan , Wang Xin , Wang Qiye , Yi Zhenfeng , Xia Jun , Hu Yuyao , Zhang Yiming , Wang Jingjing , Wang Lei , Jiang Shuzhong , Li Rong , Wan Dan , Yang Huansheng , Yin Yulong 
Published: January 2021

AbstractThis study investigated the different addition levels of iron (Fe) in growing-finishing pigs and the effect of different Fe levels on growth performance, hematological status, intestinal barrier function, and intestinal digestion. A total of 1,200 barrows and gilts ([Large White × Landrace] × Duroc) with average initial body weight (BW; 27.74 ± 0.28 kg) were housed in 40 pens of 30 pigs per pen (gilts and barrows in half), blocked by BW and gender, and fed five experimental diets (eight replicate pens per diet). The five experimental diets were control diet (basal diet with no FeSO4 supplementation), and the basal diet being supplemented with 150, 300, 450, or 600 mg/kg Fe as FeSO4 diets. The trial lasted for 100 d and was divided into the growing phase (27 to 60 kg of BW) for the first 50 d and the finishing phase (61 to 100 kg of BW) for the last 50 d. The basal diet was formulated with an Fe-free trace mineral premix and contained 203.36 mg/kg total dietary Fe in the growing phase and 216.71 mg/kg in the finishing phase based on ingredient contributions. And at the end of the experiment, eight pigs (four barrows and four gilts) were randomly selected from each treatment (selected one pig per pen) for digesta, blood, and intestinal samples collection. The results showed that the average daily feed intake (P = 0.025), average daily gain (P = 0.020), and BW (P = 0.019) increased linearly in the finishing phase of pigs fed with the diets containing Fe. On the other hand, supplementation with different Fe levels in the diet significantly increased serum iron and transferrin saturation concentrations (P &lt; 0.05), goblet cell numbers of duodenal villous (P &lt; 0.001), and MUC4 mRNA expression (P &lt; 0.05). The apparent ileal digestibility (AID) of amino acids (AA) for pigs in the 450 and 600 mg/kg Fe groups was greater (P &lt; 0.05) than for pigs in the control group. In conclusion, dietary supplementation with 450 to 600 mg/kg Fe improved the growth performance of pigs by changing hematological status and by enhancing intestinal goblet cell differentiation and AID of AA.
Laboratory Oviposition Choice ofAedes aegypti(Diptera: Culicidae) From Kenya and Gabon: Effects of Conspecific Larvae, Salinity, Shading, and Microbiome
Authors: Xia Siyang 
Published: January 2021

AbstractThe mosquito Aedes aegypti (L.) is the primary vector of several arboviruses. Mosquito control and surveillance are essential to restrict disease transmission, the effectiveness of which depends on our understanding of the mosquito’s behaviors, including oviposition. Previous studies have identified a variety of oviposition cues. However, most of these studies involved only Ae. aegypti outside of the species’ native range, Africa. Populations outside Africa differ in their genetics and some behaviors from their African counterparts, suggesting possibly different oviposition preferences. Within Africa, Ae. aegypti can be found in both ancestral forest habitats and domestic habitats. The African domestic populations may represent an intermediate state between the forest and the truly domesticated non-African populations. Comparing mosquitoes from these three habitats (African forest, African domestic, and non-African domestic) might provide insight into the evolution of oviposition behavior. In this study, I examined the oviposition choices of multiple Ae. aegypti colonies from all three habitats in laboratory settings. I applied a two-choice assay to test four oviposition cues: the preexistence of conspecific larvae, salinity, shading, and microbiome. A subset of African colonies showed similar oviposition choices as their non-African counterparts, whereas the rest show little response to the factors tested. Within the African colonies, oviposition choices of the domestic colonies were significantly different from the forest colonies in most experiments. Yet, their preferences were not always intermediate between that of mosquitoes from the other two habitats. Collectively, this study adds to our understanding of Ae. aegypti oviposition, especially in previously understudied African populations.
Surveillance of Ticks and Tick-Borne Pathogens in Suburban Natural Habitats of Central Maryland
Authors: Milholland Matthew T , Eisen Lars , Nadolny Robyn M , Hojgaard Andrias , Machtinger Erika T , Mullinax Jennifer M , Li Andrew Y 
Published: January 2021

AbstractLyme and other tick-borne diseases are increasing in the eastern United States and there is a lack of research on integrated strategies to control tick vectors. Here we present results of a study on tick-borne pathogens detected from tick vectors and rodent reservoirs from an ongoing 5-yr tick suppression study in the Lyme disease-endemic state of Maryland, where human-biting tick species, including Ixodes scapularis Say (Acari: Ixodidae) (the primary vector of Lyme disease spirochetes), are abundant. During the 2017 tick season, we collected 207 questing ticks and 602 ticks recovered from 327 mice (Peromyscus spp. (Rodentia: Cricetidae)), together with blood and ear tissue from the mice, at seven suburban parks in Howard County. Ticks were selectively tested for the presence of the causative agents of Lyme disease (Borrelia burgdorferi sensu lato [s.l.]), anaplasmosis (Anaplasma phagocytophilum), babesiosis (Babesia microti), ehrlichiosis (Ehrlichia ewingii, Ehrlichia chaffeensis, and ‘Panola Mountain’ Ehrlichia) and spotted fever group rickettsiosis (Rickettsia spp.). Peromyscus ear tissue and blood samples were tested for Bo. burgdorferi sensu stricto (s.s), A. phagocytophilum, Ba. microti, and Borrelia miyamotoi. We found 13.6% (15/110) of questing I. scapularis nymphs to be Bo. burgdorferi s.l. positive and 1.8% (2/110) were A. phagocytophilum positive among all sites. Borrelia burgdorferi s.s. was found in 71.1% (54/76) of I. scapularis nymphs removed from mice and 58.8% (194/330) of captured mice. Results from study on tick abundance and pathogen infection status in questing ticks, rodent reservoirs, and ticks feeding on Peromyscus spp. will aid efficacy evaluation of the integrated tick management measures being implemented.
Effect of Incisional Negative Pressure Wound Therapy vs Standard Wound Dressing on the Development of Surgical Site Infection after Spinal Surgery: A Prospective Observational Study
Authors: Mueller Kyle B , D’Antuono Matthew , Patel Nirali , Pivazyan Gnel , Aulisi Edward F , Evans Karen K , Nair M Nathan 
Published: January 2021

Abstract

BACKGROUND
Use of a closed-incisional negative pressure therapy (ci-NPT) dressing is an emerging strategy to reduce surgical site infections (SSIs) in spine surgery that lacks robust data.

OBJECTIVE
To determine the impact of a ci-NPT, as compared with a standard dressing, on the development of SSIs after spine surgery.

METHODS
This was a prospective observational study over a 2-yr period. Indications for surgery included degenerative disease, deformity, malignancy, and trauma. Exclusion criteria included anterior and lateral approaches to the spine, intraoperative durotomy, or use of minimally invasive techniques. SSIs up to 60 d following surgery were recorded.

RESULTS
A total of 274 patients were included. SSI rate was significantly lower with ci-NPT dressing (n = 118) as compared with the standard dressing (n = 156) (3.4 vs 10.9%, P = .02). There was no statistical difference in infection rate for decompression alone procedures (4.2 vs 9.1%, P = .63), but there was a statistically significant reduction with the use of a negative-pressure dressing in cases that required instrumentation (3.2 vs 11.4%, P = .03). Patients at higher risk (instrumentation, deformity, and malignancy) had less SSIs with the use of ci-NPT, although this did not reach statistical significance. There were no complications in either group.

CONCLUSION
SSI rates were significantly reduced with a ci-NPT dressing vs a standard dressing in patients who underwent spinal surgery. The higher cost of a ci-NPT dressing might be justified with instrumented cases, as well as with certain high-risk patient populations undergoing spine surgery, given the serious consequences of an infection.
Fruit and Vegetable Dietary Patterns and Mental Health in Women: A Systematic Review
Authors: Guzek Dominika , Gła¸bska Dominika , Groele Barbara , Gutkowska Krystyna 
Published: January 2021

Abstract

Context
Mental health may be influenced by some dietary patterns. Among common elements of beneficial patterns is high fruit and vegetable intake. However, no systematic review has been conducted to date, to our knowledge, that has assessed the influence of fruit and vegetable dietary patterns on a broad spectrum of mental health.

Objective
We conducted a systematic review, using the PRISMA guidelines, of the observational studies analyzing the association between the dietary pattern of fruit and vegetables and the broad aspects of mental health in adult women.

Data sources
The databases PubMed and Web of Science were searched, and additional manual search for observational peer-reviewed studies was conducted for studies published until June 2019.

Data extraction
A total of 5911 studies were extracted and verified based on title and abstract for the inclusion criteria. All procedures were conducted independently by 2 researchers. The final number of included studies was 30. The review was structured around the type of observed outcome.

Data analysis
The included studies had defined habitual intake associated with dietary patterns with the intake of specific fruit and/or vegetables, and/or fruit or vegetable products (eg, juices), as well as any aspect of the broad spectrum of general mental health. The Newcastle–Ottawa Scale was used to assess bias. The observed association was not stated in all the included studies; some of them revealed a reverse relationship, but only for the vegetarian/vegan diet. A vegetarian diet may be characterized by high consumption of fruits and vegetables, but it sometimes may not be properly balanced, due to excluded products. This may be the reason of observed situation.

Conclusions
A general positive influence was observed for the dietary patterns characterized by high consumption of fruit and vegetables and of fruit or vegetable products by women.

Systematic review registration
PROSPERO registration no. CRD42019138148.
Comparative Analysis of Capillary vs Venous Blood for Serologic Detection of SARS-CoV-2 Antibodies by RPOC Lateral Flow Tests
Authors: Morshed Muhammad , Sekirov Inna , McLennan Meghan , Levett Paul N , Chahil Navdeep , Mak Annie , Carruthers Erin , Pidduck Tamara , Kustra Jesse , Laley Jonathan , Lee Min-Kuang , Chu Kenneth , Burgess Fred , Vijh Rohit , Willis Lori , Wada Ray , Blancaflor Rosemarie , Boraston Suni , Hayden Althea , Krajden Mel 
Published: January 2021

Abstract
A comparison of rapid point-of-care serology tests using finger prick and venous blood was done on 278 participants. In a laboratory setting, immunoglobulin G (IgG) sensitivity neared 100%; however, IgG sensitivity dramatically dropped (82%) in field testing. Possible factors include finger prick volume variability, hemolysis, cassette readability, and operator training.
Gorham Stout disease: a case report from Syria
Authors: Esper Asil , Alhoulaiby Sami , Emran Areege , Youssef Safwan , Alshehabi Zuheir 
Published: January 2021

Abstract
Gorham-Stout disease (GSD) is a rare entity that destroys the bone matrix resulting mainly in osteolysis, pain and pathologic fractures among a broader clinical picture. We report a case of a 60-year-old female with a sudden discovery of pathologic fractures in the pelvis and the absence of the left femoral head. On biopsy, no cellular atypia was found, instead disturbed bone formation with prominent vascularity with scattered foci of necrosis & osteolysis, which lead to the diagnosis of GSD. Possible differential diagnoses were discussed and excluded. The patient was put on Bisphosphonate that led to a relative improvement in the symptoms. This disease needs a more thorough investigation to identify the key cause, what is beyond the scope of this report.