bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and application of a fast and efficient CRISPR-based genetic toolkit in Bacillus amyloliquefaciens LB1ba02
Authors: Xin Qinglong , Chen Yudan , Chen Qianlin , Wang Bin , Pan Li 
Published: May 2022

AbstractBackgroundBacillus amyloliquefaciensis generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry.B.amyloliquefaciensLB1ba02 is a production strain suitable for secreting mesophilic α-amylase in the industry. Nevertheless, due to the low transformation efficiency and restriction-modification system, the development of its CRISPR tool lags far behind other species and strains from the genusBacillus. This work was undertaken to develop a fast and efficient gene-editing tool inB.amyloliquefaciensLB1ba02.ResultsIn this study, we fused the nuclease-deficient mutant Cas9n (D10A) of Cas9 with activation-induced cytidine deaminase (AID) and developed a fast and efficient base editing system for the first time inB. amyloliquefaciensLB1ba02. The system was verified by inactivating thepyrFgene coding orotidine 5'-phosphate decarboxylase and the mutant could grow normally on M9 medium supplemented with 5-fluoroorotic acid (5-FOA) and uridine (U). Our base editing system has a 6nt editing window consisting of an all-in-one temperature-sensitive plasmid that facilitates multiple rounds of genome engineering inB. amyloliquefaciensLB1ba02. The total editing efficiency of this method reached 100% and it achieved simultaneous editing of three loci with an efficiency of 53.3%. In addition, based on the base editing CRISPR/Cas9n-AID system, we also developed a single plasmid CRISPR/Cas9n system suitable for rapid gene knockout and integration. The knockout efficiency for a single gene reached 93%. Finally, we generated 4 genes (aprE,nprE,wprA, andbamHIR) mutant strain, LB1ba02△4. The mutant strain secreted 1.25-fold more α-amylase into the medium than the wild-type strain.ConclusionsThe CRISPR/Cas9n-AID and CRISPR/Cas9n systems developed in this work proved to be a fast and efficient genetic manipulation tool in a restriction-modification system and poorly transformable strain.
Setting foot in private spaces: extending the hepatitis C cascade of care to automatic needle/syringe dispensing machines, a mixed methods study
Authors: Coupland Heidi , Henderson Charles , Pritchard-Jones Janice , Kao Shih-Chi , Sheils Sinead , Nagy Regina , O’Donnell Martin , Haber Paul S. , Day Carolyn A. 
Published: May 2022

Abstract
Background
Global commitment to achieving hepatitis C virus (HCV) elimination has enhanced efforts in improving access to direct-acting antiviral (DAA) treatments for people who inject drugs (PWID). Scale-up of efforts to engage hard-to-reach groups of PWID in HCV testing and treatment is crucial to success. Automatic needle/syringe dispensing machines (ADMs) have been used internationally to distribute sterile injecting equipment. ADMs are a unique harm reduction service, affording maximum anonymity to service users. This paper explores the feasibility and acceptability of extending the HCV cascade of care to sites where ADMs are located.

Methods
The ADM users into Treatment (ADMiT) study was undertaken in a metropolitan region in Sydney, Australia. This mixed methods study involved analysis of closed-circuit television footage, ethnographic methods (fieldwork observation and in-depth interviews) and structured surveys. Researchers and peers conducted fieldwork and data collection over 10 weeks at one ADM site, including offering access to HCV testing and treatment.

Results
Findings from 10 weeks of fieldwork observations, 70 survey participants and 15 interviews highlighted that there is scope for engaging with this population at the time they use the ADM, and enhanced linkage to HCV testing and treatment may be warranted. Most survey participants reported prior HCV testing, 61% in the last 12 months and 38% had received HCV treatment. However, fieldwork revealed that most people observed using the ADM were not willing to engage with the researchers. Field work data and interviews suggested that extending the HCV cascade of care to ADMs may encroach on what is a private space for many PWID, utilized specifically to avoid engagement.

Discussion
Enhanced linkage to HCV testing and treatment for people who use ADMs may be warranted. However, data suggested that extending the HCV cascade of care to ADMs may encroach on what is a private space for many PWID, utilized specifically to avoid engagement. The current study raises important public health questions about the need to ensure interventions reflect the needs of affected communities, including their right to remain anonymous.
Risky sexual behavior and associated factors among sexually-experienced adolescents in Bangkok, Thailand: findings from a school web-based survey
Authors: Thepthien Bang-on , Celyn  
Published: May 2022

Abstract
Background
The risk of sexually transmitted infections (STI) arises when there is unsafe sexual activity. Unsafe sex often begins in the teenage years, and it will persist as long as there is the opportunity for risky sexual activity. The purpose of this study was to assess the sexual risk behaviors and related factors of sexually-active adolescents in educational institutions in Thailand.

Methods
This was cross-sectional survey using an Internet-based application in schools in Bangkok from November 2020 to February 2021 with a total of 6,167 high school and vocational students. The schools were selected by simple random sampling among institutions, and the students were systematically randomly selected, with an equal number of males and females. We used multivariable logistic regression to analyze associations and control confounding variables. Indicators of risky sex include: (1) Not using a condom; (2) Having more than one sex partner; (3) Having sex in exchange for cash or in-kind compensation; and (4) Having sex without consent.

Results
Of a total of 872 sexually-active participants, the mean age was 15.6 years, 66.9% were vocational students, 42.1% were male, 57.9% were female, and 69.5% had sex risk behavior. The multivariate logistic regression analysis identified the following statistically-significant factors related to risky sex: smokes cigarettes (AOR = 1.79; 95% CI 1.12–2.88); uses cannabis (AOR = 2.84; 95% CI 1.23–6.56); gambles (AOR = 1.81; 95% CI 1.28–2.55); has sex without contraception (AOR = 2.74; 95% CI 2.91–3.93); has a history of childhood sex abuse (AOR = 1.60; 95% CI 1.03–2.56).

Conclusions
Our findings suggest that, in designing and implementing sexual risk prevention programs for adolescents in educational settings, there is a need to highlight the role of substance abuse in relation to sexual risk behaviors. Programs should target both male and female students. Teenagers who use marijuana are more likely to be sexually active than those who have never used marijuana. These potential risks should be taken into account with respect to legalization of marijuana and recreational use of this drug.
Microbial spore genetic marker technology, a potential technology for traditional Chinese medicine traceability system
Authors: Zhao Dazhong , Tian Zunzhe , Cai Jing , He Juan 
Published: May 2022

AbstractTraditional Chinese medicine (TCM) has a long history, rich clinical experience, and unique advantages in the prevention and treatment of diseases. The quality and safety of Chinese medicinal materials (CMMs) directly affect the clinical efficacy and development of the TCM industry. However, confused provenance, counterfeiting and adulteration of CMMs hinder the acceptance of its therapeutic benefits in modern society. Therefore, the establishment and improvement of a TCM traceability system would be conducive to the transparency of the CMMs production, distribution, and circulation, thereby improving drug safety and promoting industry development. This review discusses the challenges faced in the development of TCM traceability system, the technologies currently available for tracing CMMs, and the potential application of Barcoded Microbial Spores (BMS) to improve CMMs origin traceability and TCM traceability systems.
Ma’s bamboo-based medicinal moxibustion therapy of low back pain in lumbar disc herniation: study protocol for a randomized controlled trial
Authors: Wang Xian-zhu , Xue Kai-yang , Chen Ping-nan , Xiao Cai-hong , Cui Jin , Fu Jing 
Published: May 2022

Abstract
Background
Lumbar disc herniation (LDH) is a common and frequently occurring disease in clinics. Low back pain and sciatica are the presenting symptoms of LDH. To some extent, it can be considered that measures with the capability to improve low back pain or sciatica have the potential to treat LDH. Ma’s bamboo-based medicinal moxibustion therapy can effectively reduce the degree of low back pain and has been widely used. Studies of small sample size have seen significant improvement on pain relief. The aim of this trial is to evaluate the clinical efficacy and safety of Ma’s bamboo-based medicinal moxibustion therapy in the treatment of LDH low back pain.

Methods/design
The trial is a multicenter, randomized, parallel-group, non-inferiority study. Three hundred and twelve patients will be randomly assigned to a Ma’s bamboo-based medicinal moxibustion group (n=156) and an acupuncture group (n=156). Patients in each group will receive treatment every day, 6 times a week, 12 times in total. Follow-up will be conducted 14 days after treatment. The primary outcome will be the visual analog scale(VAS) at baseline, after 6 times of treatment, end of treatment, and follow-up. The secondary outcomes will include Oswestry disability indexes (ODI), modified Japanese Orthopaedic Association low back pain (M-JOA) score, serum β-endorphin (β-EP), and serum substance P (SP). β-EP and SP, as well as safety evaluation indexes (routine blood, liver, and kidney function and electrocardiogram), will be measure at baseline and after the end of treatment. The number, nature, and severity of adverse events will be recorded.

Discussion
The results of the trial will compare the efficacy of low back pain in LDH between Ma’s bamboo-based medicinal moxibustion group and the acupuncture group and will be expected to make a systematic and objective evaluation of the clinical efficacy and safety of Ma’s bamboo-based medicinal moxibustion therapy.

Trial registration
ChiCTR2000038725. Registered on 29 September 2020.
Viral histones: pickpocket’s prize or primordial progenitor?
Authors: Talbert Paul B. , Armache Karim-Jean , Henikoff Steven 
Published: May 2022

AbstractThe common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA and compact the genome as well as to regulate access to DNA for transcription and replication in all eukaryotes. In the past two decades, histones have also been found to be encoded in some DNA viruses, where their functions and properties are largely unknown, though recently histones from two related viruses have been shown to form nucleosome-like structures in vitro. Viral histones can be highly similar to eukaryotic histones in primary sequence, suggesting they have been recently picked up from eukaryotic hosts, or they can be radically divergent in primary sequence and may occur as conjoined histone doublets, triplets, or quadruplets, suggesting ancient origins prior to the divergence of modern eukaryotes. Here, we review what is known of viral histones and discuss their possible origins and functions. We consider how the viral life cycle may affect their properties and histories, and reflect on the possible roles of viruses in the origin of the nucleus of modern eukaryotic cells.
Lifetime exposure to smoking, epigenetic aging, and morbidity and mortality in older adults
Authors: Klopack Eric T. , Carroll Judith E. , Cole Steve W. , Seeman Teresa E. , Crimmins Eileen M. 
Published: May 2022

Abstract
Background
Cigarette smoke is a major public health concern. Epigenetic aging may be an important pathway by which exposure to cigarette smoke affects health. However, little is known about how exposure to smoke at different life stages affects epigenetic aging, especially in older adults. This study examines how three epigenetic aging measures (GrimAge, PhenoAge, and DunedinPoAm38) are associated with parental smoking, smoking in youth, and smoking in adulthood, and whether these epigenetic aging measures mediate the link between smoke exposure and morbidity and mortality. This study utilizes data from the Health and Retirement Study (HRS) Venous Blood Study (VBS), a nationally representative sample of US adults over 50 years old collected in 2016. 2978 participants with data on exposure to smoking, morbidity, and mortality were included.

Results
GrimAge is significantly increased by having two smoking parents, smoking in youth, and cigarette pack years in adulthood. PhenoAge and DunedinPoAm38 are associated with pack years. All three mediate some of the effect of pack years on cancer, high blood pressure, heart disease, and mortality and GrimAge and DunedinPoAm38 mediate this association on lung disease.

Conclusions
Results suggest epigenetic aging is one biological mechanism linking lifetime exposure to smoking with development of disease and earlier death in later life. Interventions aimed at reducing smoking in adulthood may be effective at weakening this association.
Novel genetic variants of KHDC3L and other members of the subcortical maternal complex associated with Beckwith–Wiedemann syndrome or Pseudohypoparathyroidism 1B and multi-locus imprinting disturbances
Authors: Pignata Laura , Cecere Francesco , Verma Ankit , Hay Mele Bruno , Monticelli Maria , Acurzio Basilia , Giaccari Carlo , Sparago Angela , Hernandez Mora Jose Ramon , Monteagudo-Sánchez Ana , Esteller Manel , Pereda Arrate , Tenorio-Castano Jair , Palumbo Orazio , Carella Massimo , Prontera Paolo , Piscopo Carmelo , Accadia Maria , Lapunzina Pablo , Cubellis Maria Vittoria , de Nanclares Guiomar Perez , Monk David , Riccio Andrea , Cerrato Flavia 
Published: May 2022

Abstract
Background
Beckwith–Wiedemann syndrome (BWS) and Pseudohypoparathyroidism type 1B (PHP1B) are imprinting disorders (ID) caused by deregulation of the imprinted gene clusters located at 11p15.5 and 20q13.32, respectively. In both of these diseases a subset of the patients is affected by multi-locus imprinting disturbances (MLID). In several families, MLID is associated with damaging variants of maternal-effect genes encoding protein components of the subcortical maternal complex (SCMC). However, frequency, penetrance and recurrence risks of these variants are still undefined. In this study, we screened two cohorts of BWS patients and one cohort of PHP1B patients for the presence of MLID, and analysed the positive cases for the presence of maternal variants in the SCMC genes by whole exome-sequencing and in silico functional studies.

Results
We identified 10 new cases of MLID associated with the clinical features of either BWS or PHP1B, in which segregate 13 maternal putatively damaging missense variants of the SCMC genes. The affected genes also included KHDC3L that has not been associated with MLID to date. Moreover, we highlight the possible relevance of relatively common variants in the aetiology of MLID.

Conclusion
Our data further add to the list of the SCMC components and maternal variants that are involved in MLID, as well as of the associated clinical phenotypes. Also, we propose that in addition to rare variants, common variants may play a role in the aetiology of MLID and imprinting disorders by exerting an additive effect in combination with rarer putatively damaging variants. These findings provide useful information for the molecular diagnosis and recurrence risk evaluation of MLID-associated IDs in genetic counselling.
Allergic shiners in a patient with cough-variant asthma: a case report
Authors: Rekabi Mahsa , Raad Nasim , Abedini Atefeh , Darougar Sepideh , Velayati Ali Akbar 
Published: May 2022

Abstract
Background
Chronic cough, with a duration of coughing of more than 8 weeks in adults, affects 5–10% of the general population. One of the most common causes of chronic cough is cough-variant asthma, which accounts for approximately one-third of cases. This phenotype of asthma is characterized by extreme sensitivity of the neuronal pathways mediating cough to environmental irritants, which results in an urge to cough. This case is an example of cough-variant asthma presenting with allergic shiners due to her severe cough.

Case presentation
A 38-year-old Iranian woman, who was well before the start of the coronavirus disease 2019 pandemic, presented with a nonproductive hacking cough that had begun after excessive use of antiseptic solutions. The only positive finding on physical examination was a reddish-purple rash on and around the eyelids mimicking a heliotrope rash, which had probably evolved due to the severity of the cough. The results of the pulmonary function test were within normal limits. Methacholine challenge test and chest x-ray were both normal. Chest high-resolution computed tomography revealed hyperinflation and tree-in-bud opacities. All other laboratory tests were normal. Because of the reversibility in her pulmonary function test, despite normal baseline parameters, asthma treatment was initiated, resulting in disappearance of the cough and the eye discoloration, being indicative of the correct diagnosis and proper treatment.

Conclusion
Patients with cough-variant asthma may often have no other classic symptoms of asthma other than cough.
Safety and efficacy of pilocarpine, cevimeline, and diquafosol compared to artificial tears for the treatment of dry eye: protocol for a systematic review
Authors: Serrano-Robles José Gerardo , Pérez Vázquez Ana Karen , Navas Alejandro , Graue-Hernandez Enrique O. , Ramirez-Miranda Arturo , Kahuam-López Nicolás 
Published: May 2022

Abstract
Background
Dry eye disease (DED) is a condition that compromises the ocular surface and affects millions of people around the world. In recent years, a scheme has been proposed for the treatment of DED, with the use of artificial tear being the mainstay of treatment. In this scheme, the use of secretagogues is suggested as part of the treatment for patients with moderate to severe affectation. With this systematic review, we aim to evaluate the effectiveness and safety of secretagogues for DED.

Methods
Electronic databases will be searched; we will include randomized controlled trials that compare secretagogues and artificial tears. Study inclusion will not be restricted on the basis of language or publication status. We will use Google Translate to assess studies written in languages other than English and Spanish. Identification, evaluation, data extraction, and assessment of risk of bias will be conducted by two authors of the review, a third review author will resolve any disagreement. The outcomes will be the ocular surface disease index score, tear film break-up time, Schirmer test score, VRQoL Score, and tear film osmolarity. We will use the Cochrane Collaboration Risk of Bias 2 (RoB 2) tool for assessing the risk of bias of the included studies.
Based on the heterogeneity of the included studies, we will combine the findings in a meta-analysis using a fixed effect model if heterogeneity ≤ 50% or a random effect model if heterogeneity > 50%. If we deem meta-analysis as inappropriate, we will document the reasons and report findings from the individual studies narratively.

Discussion
Based on the evidence obtained, we will evaluate the effect of pilocarpine, cevimeline, and diquafosol and compare it to artificial tears on multiple outcome measures.
This systematic review aims to determine the efficacy and safety of the secretagogues pilocarpine, cevimeline, and diquafosol to help clinicians in the decision-making process.

Trial registration
PROSPERO CRD42020218407.
In vitro and in planta potential effect of some indigenous antagonists against Fusarium and pythiaceous species associated with peach seedlings decline
Authors: Mannai Sabrine , Boughalleb-M’Hamdi Naima 
Published: May 2022

Abstract
Background
The effect of Aspergillus spp. and Trichoderma harzianum isolates was evaluated against the growth of Fusarium oxysporum, F. solani, Pythium ultimum and Phytophthora citrophthora affecting peach seedlings.

Results
The in vitro results revealed the ability of these antagonistic in reducing the radial growth of these pathogens. The most important mycelial growth reduction was of 85.82%, recorded for F. oxysporum in confrontation with A5 of Aspergillus candidus. Aspergillus flavus A4 and A. niger A10 were the most effective against F. solani with an inhibition percent more than 60%. For P. citrophthora, A. flavus A4, A. candidus A5, A. terreus A9 and A. niger A10 inhibited the mycelia growth by more than 60%. Aspergillus nidulans A1 was the most effective against Pythium ultimum (72.07%). Trichoderma harzianum isolates T9 and T10, are the most effective with a high inhibition percent of mycelial growth. The inhibition induced after 4 days of incubation, against F. oxysporum, F. solani, P. citrophthora and Pythium ultimum by these 2 antagonists exceeded 70, 60, 70 and 80%, respectively. The in planta test showed the efficacy of antagonists tested solo against some pathogens. In fact, Bacillus subtilis improved the health status by 62.55% compared to the control inoculated with P. ultimum. Trichoderma harzianum T9 significantly reduced the root rot index by 87.5% than the control inoculated with F. solani. In the same sense, B. subtilis significantly reduced this parameter by 62.55 and 88.89% than the control inoculated with P. ultimum and P. citrophthora, respectively. Furthermore, B. subtilis (B) and Aspergillus niger A10 improved plants height than the control inoculated with Pythium ultimum by 31.52 and 40.49%, respectively. However, the combinations of antagonists (T9 + T10; A5 + A10 and B + T10) did not improve their efficacy.

Conclusions
The isolates T. harzianum (T9 and T10), A. candidus A5 and A. niger A10 were the most effective in vitro against Fusarium, Pythium and Phytophthora species associated with peach seedling decline. The in vivo assay showed the effectiveness of B. subtilis against P. ultimum and P. citrophthora and the potential effect of T. harzianum T9 against F. solani. Their combinations revealed to be ineffective.