bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heritable gene editing using FT mobile guide RNAs and DNA viruses
Authors: Lei Jianfeng , Dai Peihong , Li Yue , Zhang Wanqi , Zhou Guantong , Liu Chao , Liu Xiaodong 
Published: February 2021

Abstract
Background
The virus-induced genome editing (VIGE) system can be used to quickly identify gene functions and generate knock-out libraries as an alternative to the virus-induced gene silencing (VIGS). Although plant virus-mediated VIGE has been shown to have great application prospects, edited genes cannot be transferred to the next generations using this system, as viruses cannot enter into shoot apical meristem (SAM) in plants.

Results
We developed a novel cotton leaf crumple virus (CLCrV)-mediated VIGE system designed to target BRI1, GL2, PDS genes, and GUS transgene in A. thaliana by transforming Cas9 overexpression (Cas9-OE) A. thaliana. Given the deficiency of the VIGE system, ProYao::Cas9 and Pro35S::Cas9 A. thaliana were transformed by fusing 102 bp FT mRNAs with sgRNAs so as to explore the function of Flowering Locus T (FT) gene in delivering sgRNAs into SAM, thus avoiding tissue culture and stably acquiring heritable mutant offspring. Our results showed that sgRNAs fused with FT mRNA at the 5′ end (FT strategy) effectively enabled gene editing in infected plants and allowed the acquisition of mutations heritable by the next generation, with an efficiency of 4.35–8.79%. In addition, gene-edited offspring by FT-sgRNAs did not contain any components of the CLCrV genome.

Conclusions
FT strategy can be used to acquire heritable mutant offspring avoiding tissue culture and stable transformation based on the CLCrV-mediated VIGE system in A. thaliana.
Evaluation of muscle volume and degeneration after total hip arthroplasty: a comparison of the posterolateral approach and the anterolateral supine approach
Authors: Ukai Taku , Ebihara Goro , Omura Haruka , Watanabe Masahiko 
Published: February 2021

Abstract
Background
Muscle strength around the hip after total hip arthroplasty (THA) is crucial for preventing dislocation and limping. This study aimed to assess and compare muscle volume and degeneration after THA using the posterolateral (PL) and anterolateral (AL) approaches.

Methods
Sixty-four hips in 64 patients who underwent primary THA were retrospectively analyzed. Patients were segregated into the PL group (35 hips) and AL group (29 hips) for evaluating pre- and postoperative muscle volumes and degeneration around the hip. Computed tomography (CT) examinations were performed preoperatively and 6 months post THA. The muscle volume and Hounsfield units (HU) of the gluteus maximus (G-max), gluteus medius (G-med), tensor fasciae latae, internal obturator muscle, and external obturator muscle were measured.

Results
In the PL group, the postoperative muscle volume of the G-max significantly increased than the preoperative muscle volume. In contrast, the postoperative muscle volume of the internal obturator muscle was significantly lower than the preoperative muscle volume. The postoperative HU of the internal and external obturator muscles were significantly lower than the preoperative HU. In the AL group, the postoperative muscle volumes of the G-max, G-med, and tensor fasciae latae significantly increased than their preoperative muscle volumes. The postoperative HU of the G-med and tensor fasciae latae were significantly higher than the preoperative HU values.

Conclusion
The PL approach can lead to degeneration of the internal and external obturator. The AL approach is more beneficial for recovering the G-med, tensor fasciae latae, and internal obturator muscle than the PL approach.
Synovial fluid IL-1β appears useful for the diagnosis of chronic periprosthetic joint infection
Authors: Wang Hai , Qin Leilei , Wang Jiawei , Huang Wei 
Published: February 2021

Abstract
Purpose
The purpose of this study was to investigate the role of synovial fluid interleukin (IL)-1β in diagnosing chronic periprosthetic joint infection (PJI) and to identify the optimal threshold of synovial fluid IL-1β for differentiating chronic PJI from aseptic failure after knee and hip arthroplasties.

Methods
Between January 2019 and December 2019, we prospectively included patients scheduled to have a revision surgery for chronic PJI or aseptic failure after total joint arthroplasty. Then, synovial IL-1β was additionally measured along with routine preoperative diagnostic serum and synovial biomarkers. The receiver operating characteristic (ROC) curves and area under the curve (AUC) were analyzed for each biomarker to determine diagnostic efficacy.

Results
Of the 93 patients included, their demographic data were not found to be statistically significant. The median synovial IL-1β levels were significantly higher in the chronic PJI group than in the aseptic group (894.73 pg/mL vs. 34.49 pg/mL, P<0.01). The AUC for synovial fluid IL-1β was 0.991, which was higher than serum ESR (0.627) and CRP (0.712). The optimal threshold value for detecting chronic PJI of synovial IL-1β was 312.7 pg/mL, with a sensitivity of 97.3% and a specificity of 94.64%. And the combined measurement of synovial fluid IL-1β and synovial fluid PMN% can led to a specificity of 1, and a negative predictive value (NPV) of 1.

Conclusions
The present study demonstrated that synovial fluid IL-1β is a valuable biomarker for detection of chronic PJI. The combination of synovial fluid IL-1β and PMN% led to an improvement in specificity compared with evaluation of each single index.

Trial registration
This study was prospectively registered on the Chinese Clinical Trial Registry (a non-profit organization, established according to both the WHO International Clinical Trials Register Platform Standard and Ottawa Group Standard), and the registering number was ChiCTR1800020440. Registered on December 29, 2018.
Epidemiology of systemic sclerosis: a multi-database population-based study in Tuscany (Italy)
Authors:   the Rare Diseases Working Group, Coi Alessio , Barsotti Simone , Santoro Michele , Almerigogna Fabio , Bargagli Elena , Caproni Marzia , Emmi Giacomo , Frediani Bruno , Guiducci Serena , Matucci Cerinic Marco , Mosca Marta , Parronchi Paola , Prediletto Renato , Selvi Enrico , Simonini Gabriele , Tavoni Antonio Gaetano , Bianchi Fabrizio , Pierini Anna 
Published: February 2021

Abstract
Background
Systemic Sclerosis (SSc) is a chronic autoimmune disease with a complex pathogenesis that includes vascular injury, abnormal immune activation, and tissue fibrosis. We provided a complete epidemiological characterization of SSc in the Tuscany region (Italy), considering prevalence and incidence, survival, comorbidities and drug prescriptions, by using a multi-database population-based approach. Cases of SSc diagnosed between 1st January 2003 and 31st December 2017 among residents in Tuscany were collected from the population-based Rare Diseases Registry of Tuscany. All cases were linked to regional health and demographic databases to obtain information about vital statistics, principal causes of hospitalization, complications and comorbidities, and drug prescriptions.

Results
The prevalence of SSc in Tuscany population resulted to be 22.2 per 100,000, with the highest prevalence observed for the cases aged ≥ 65 years (33.2 per 100,000, CI 95% 29.6–37.3). In females, SSc was predominant (86.7% on the total) with an overall sex ratio F/M of 6.5. Nevertheless, males presented a more severe disease, with a lower survival and significant differences in respiratory complications and metabolic comorbidities. Complications and comorbidities such as pulmonary involvement (HR = 1.66, CI 95% 1.17–2.35), congestive heart failure (HR = 2.76, CI 95% 1.80–4.25), subarachnoid and intracerebral haemorrhage (HR = 2.33, CI 95% 1.21–4.48) and malignant neoplasms (HR = 1.63, CI 95% 1.06–2.52), were significantly associated to a lower survival, also after adjustment for age, sex and other SSc-related complications. Disease-modifying antirheumatic drugs, endothelin receptor antagonists, and phosphodiesterase-5 inhibitors were the drugs with the more increasing prevalence of use in the 2008–2017 period.

Conclusions
The multi-database approach is important in the investigation of rare diseases where it is often difficult to provide accurate epidemiological indicators. A population-based registry can be exploited in synergy with health databases, to provide evidence related to disease outcomes and therapies and to assess the burden of disease, relying on a large cohort of cases. Building an integrated archive of data from multiple databases linking a cohort of patients to their comorbidities, clinical outcomes and survival, is important both in terms of treatment and prevention.
Deletion of Socs3 in LysM+ cells and Cx3cr1 resulted in age-dependent development of retinal microgliopathy
Authors: Du Xuan , Penalva Rosana , Little Karis , Kissenpfennig Adrien , Chen Mei , Xu Heping 
Published: February 2021

AbstractBackgroundWe generated a mouse model of primary microglial dysfunction by deleting two negative immune regulatory genes,Cx3cr1andSocs3(in LysM+cells). This study aimed to understand how primary microglial dysfunction impacts retinal neurons during aging.MethodsTheLysMCre-Socs3fl/flCx3cr1gfp/gfpdouble knockout (DKO),LysMCre-Socs3fl/fl,Cx3cr1gfp/gfpandSocs3fl/flmice were maintained up to 12 months. Eyes were collected and processed for immunohistochemistry of IBA-1, cone arrestin, secretagogin, PKCα and GABA. Brain microglia from DKO and WT mice were stimulated with LPS + IFN-γ or IL-4. The expression of TNF-α, IL-1β, IL-6, iNOS, IL-12p40, IL-23p19, CCL2, CCL5, CXCL2, IL-10, CD206 and Arg1 were examined by qRT-PCR and protein production was measured by Luminex assay. Retinal explants from C57BL/6 J mice were co-cultured with microglia from DKO or WT mice for 24 h, after which the number of cone arrestin+cells in retinal flatmount were quantified.ResultsIn 3–5 month old mice, the number of microglia in retinal ganglion cell layer (GCL) and inner plexiform layer (IPL) were comparable in all strains of mice. The DKO mice had a significantly higher number of microglia in the outer plexiform layer (OPL) but significantly lower numbers of cone arrestin+, secretagogin+and GABA+cells compared toSocs3fl/fland single KO mice. During aging, 57% of the DKO mice died before 12 months old. The 10–12 months old DKO mice had significantly higher numbers of microglia in GCL/IPL and OPL than age-matchedSocs3fl/fland single KO mice. The aged DKO mice developed retinal pigment epithelial (RPE) dysmorphology accompanied by subretinal microglial accumulation. The number of photoreceptors, bipolar cells (Secretagogin+or PKCα+) and GABA+amacrine cells was significantly lower in aged DKO mice compared to age-matchedSocs3fl/fland single KO mice. Microglia from DKO mice showed significantly higher levels of phagocytic activity and produced higher levels of TNF-α, IL-6, CCL2, CCL5, CXCL2 and CXCL10 compared to microglia fromSocs3fl/flmice. Co-culture of retinal explants with LPS + IFN-γ or IL-4 pre-treated DKO microglia significantly reduced cone photoreceptor survival.ConclusionsTheLysMCre-Socs3fl/flCx3cr1gfp/gfpDKO mice displayed primary microglial dysfunction and developed age-related retinal microgliopathy characterized by aggragated microglial activation and multiple retinal neuronal and RPE degeneration.Trial registrationNot applicable. The article does not contain any results from human participants.
Optimized expression of Hfq protein increases Escherichia coli growth
Authors: VO Phuong N. L. , LEE Hyang-Mi , REN Jun , NA Dokyun 
Published: February 2021

AbstractEscherichia coli is a widely used platform for metabolic engineering due to its fast growth and well-established engineering techniques. However, there has been a demand for faster-growing E. coli for higher production of desired substances. Here, to increase the growth of E. coli cells, we optimized the expression level of Hfq protein, which plays an essential role in stress responses. Six variants of the hfq gene with a different ribosome binding site sequence and thereby a different expression level were constructed. When the Hfq expression level was optimized in DH5α, its growth rate was increased by 12.1% and its cell density was also increased by 4.5%. RNA-seq and network analyses revealed the upregulation of stress response genes and metabolic genes, which increases the tolerance against pH changes. When the same strategy was applied to five other E. coli strains (BL21 (DE3), JM109, TOP10, W3110, and MG1655), all their growth rates were increased by 18–94% but not all their densities were increased (− 12 − + 32%). In conclusion, the Hfq expression optimization can increase cell growth rate and probably their cell densities as well. Since the hfq gene is highly conserved across bacterial species, the same strategy could be applied to other bacterial species to construct faster-growing strains.
Potential therapeutic targets in the tumor microenvironment of hepatocellular carcinoma: reversing the protumor effect of tumor-associated macrophages
Authors: Zhou Jingyi , Wang Weiyu , Li Qi 
Published: February 2021

AbstractIn hepatocellular carcinoma patients, due to the microenvironmental specificity of liver, the tumor microenvironment exhibits high immunosuppression and drug resistance, resulting in excessive or insufficient responses to immunotherapy. The dynamic interactions between tumor cells and immune modulators in the TME significantly impact the occurrence and development of tumors, efficacy, and drug resistance, which can create a much more positive response to immunotherapy. Moreover, with the wide application of single-cell sequencing technology in the TME, increasing evidence shows an interaction network among cells. Sequencing results suggest that specific tumor-associated macrophages are a hub node, connecting different cell populations in the cell interaction network, and can could regulate tumor generation and antitumor immunity. This review focused on therapeutic targets that could be targeted to remodel the tumor microenvironment and reprogram the tumor-associated macrophage phenotype in hepatocellular carcinoma patients, thereby improving immunotherapeutic efficacy.
The effect of a topical combination of clonidine and pentoxifylline on post-traumatic neuropathic pain patients: study protocol for a randomized, double-blind placebo-controlled trial
Authors: Fulas Oli Abate , Laferrière André , Ware D. Mark A. , Shir Yoram , Coderre Terence J. 
Published: February 2021

Abstract
Background
First-line pharmacotherapy for neuropathic pain entails the use of systemic antidepressants and anticonvulsants. These drugs are not optimally effective and poorly tolerated, especially for older patients with comorbid conditions. Given the high number of such patients, there is a need for a greater repertoire of safer and more effective analgesics. Clonidine and pentoxifylline are vasodilator agents that work synergistically to enhance tissue perfusion and oxygenation. The topical administration of these drugs, individually and in combination, has shown anti-nociceptive properties in rodent models of neuropathic pain. A topically-administered combination of clonidine and pentoxifylline also effectively reduced the intensity of both spontaneous and evoked pain in healthy volunteers with experimentally-induced neuropathic pain. The next step in advancing this formulation to clinical use is the undertaking of a phase II clinical study to assess its efficacy and safety in neuropathic pain patients.

Methods/design
This is a study protocol for a randomized, double-blind, placebo-controlled, phase II clinical trial with a cross-over design. It is a single-centered, 5-week study that will enroll a total of 32 patients with post-traumatic peripheral neuropathic pain. Patients will be treated topically with either a combination of clonidine and pentoxifylline or placebo for a period of 2 weeks each, in randomly assigned order across patients, with an intervening washout period of 1 week. The primary outcome measures of the study are the intensity of spontaneous pain recorded daily in a pain diary with a visual analog scale, and the degree of mechanical allodynia evoked by a brush stimulus. The secondary outcome measures of the study include scores of pain relief and change in the area of punctate hyperalgesia. This trial has been prospectively registered with ClinicalTrials.gov on November 1, 2017. ClinicalTrials.gov Identifier: NCT03342950.

Discussion
The analgesic use of topical treatment with clonidine and pentoxifylline in combination has not been investigated in post-traumatic neuropathic pain. This study could generate the first evidence for the efficacy and safety of the formulation in alleviating pain in patients with neuropathic pain. Furthermore, this trial will provide objective grounds for the investigation of other agents that enhance tissue oxygenation in the topical treatment of peripheral neuropathic pain.

Trial registration
This trial has been registered with ClinicalTrials.gov owned by NIH’s US National Library of Medicine.
ClinicalTrials.gov NCT03342950. Registered on November 1, 2017 (trial was prospectively registered).

Protocol version and identifiers
This is protocol version 5, dated June 2018. McGill University Health Center (MUHC) Reaseach Ethics Board (REB) identification number: TTNP 2018-3906.
Host–parasite interactions of rodent hosts and ectoparasite communities from different habitats in Germany
Authors: Obiegala Anna , Arnold Leonie , Pfeffer Martin , Kiefer Matthias , Kiefer Daniel , Sauter-Louis Carola , Silaghi Cornelia 
Published: February 2021

AbstractBackgroundSmall mammals are important maintenance hosts of ectoparasites as well as reservoir hosts for many arthropod-borne pathogens. In Germany, only a few studies have investigated ectoparasite communities on small mammals in their natural habitats. The aim of this study was to assess the species diversity and parameters influencing the mean intensity and prevalence of macroscopically visible ectoparasites, such as fleas, predatory mites and ticks.MethodsA total of 779 small mammals and 3383 ticks were available from earlier investigations for the data analysis of the current study from three differently structured study sites. In addition, fleas and predatory mites were collected from the captured rodents and taxonomically identified. Regression analyses were conducted on the group (ticks/mites/fleas) and species levels using hurdle models for the abundance of ectoparasite groups and a negative binomial model for the abundance of species.ResultsNearly 90% of the small mammals analyzed were infested with ectoparasites, with an average of 7.3 specimens per host. Hosts were infested with up to six species of ectoparasites simultaneously. In total, 12 flea, 11 mite and three tick species were detected. Ticks were more prevalent than fleas or mites, with > 80% of the hosts in urban and forest areas hosting ticks and around 60% of hosts presenting fleas, and only 20–40% of hosts presenting mites. Polyparasitism had a statistically significant influence on the prevalence of the investigated tick, mite and flea species, with odds ratios of > 1.0. Trapping location, season and host characteristics had significant influences on some—but not all—of the investigated species.ConclusionsThe diversity of flea species was unexpectedly high and higher than that reported in comparable studies, which can be explained by the differently structured habitats and regions examined in this study. Polyparasitism was a key influencing factor and had a positive effect on the prevalence and/or abundance of the predominant tick, flea and mite species occurring on small mammals. Season, trapping location, host species and sex of the host species also had an influence on the prevalence and mean intensity of certain, but not all, ectoparasite species.Graphical Abstract
GCKR common functional polymorphisms are associated with metabolic syndrome and its components: a 10-year retrospective cohort study in Iranian adults
Authors: Zahedi Asiyeh Sadat , Akbarzadeh Mahdi , Sedaghati-Khayat Bahareh , Seyedhamzehzadeh Atefeh , Daneshpour Maryam S. 
Published: February 2021

Abstract
Background
Previous studies reported that common functional variants (rs780093, rs780094, and rs1260326) in the glucokinase regulator gene (GCKR) were associated with metabolic syndrome despite the simultaneous association with the favorable and unfavorable metabolic syndrome components. We decided to evaluate these findings in a cohort study with a large sample size of Iranian adult subjects, to our knowledge for the first time. We investigated the association of the GCKR variants with incident MetS in mean follow-up times for nearly 10 years.

Methods
Analysis of this retrospective cohort study was performed among 5666 participants of the Tehran Cardiometabolic Genetics Study (TCGS) at 19–88 years at baseline. Linear and logistic regression analyses were used to investigate the metabolic syndrome (JIS criteria) association and its components with rs780093, rs780094, and rs1260326 in an additive genetic model. Cox regression was carried out to peruse variants’ association with the incidence of metabolic syndrome in the TCGS cohort study.

Results
In the current study, we have consistently replicated the association of the GCKR SNPs with higher triglyceride and lower fasting blood sugar levels (p < 0.05) in Iranian adults. The CT genotype of the variants was associated with lower HDL-C levels. The proportional Cox adjusted model regression resulted that TT carriers of rs780094, rs780093, and rs1260326 were associated with 20%, 23%, and 21% excess risk metabolic syndrome incidence, respectively (p < 0.05).

Conclusions
Elevated triglyceride levels had the strongest association with GCKR selected variants among the metabolic syndrome components. Despite the association of these variants with decreased fasting blood sugar levels, T alleles of the variants were associated with metabolic syndrome incidence; so whether individuals are T allele carriers of the common functional variants, they have a risk factor for the future incidence of metabolic syndrome.
Characteristics of patients infected with Clostridioides difficile at a Saudi Tertiary Academic Medical Center and assessment of antibiotic duration
Authors: Alammari Khadijah M. , Thabit Abrar K. 
Published: February 2021

Abstract
Background
Clostridioides difficile infection (CDI) is a common hospital-associated diarrhea. Several antibiotics commonly associate with CDI; however, limited data are available on the duration of exposure prior to CDI. Moreover, studies on the characteristics of CDI patients in Saudi Arabia are limited. Therefore, this study aimed to characterize CDI patients identified over 10 years and assess antibiotic days of therapy (DOT) prior to CDI.

Methods
This was a retrospective descriptive analysis of CDI patients at a Saudi tertiary academic medical center between December 2007 and January 2018. Patients characteristics, prior exposure to known CDI risk factors, and DOT of antibiotics prior to CDI incidence were assessed.

Results
A total of 159 patients were included. Median age was 62 years. Most cases were hospital-acquired (71.1%), non-severe (44.7%), and admitted to medical wards (81.1%). Prior exposure to antibiotics and acid suppression therapy were reported with the majority (76.1 and 75.5%, respectively). The most frequently prescribed antibiotics were piperacillin/tazobactam, ceftriaxone, meropenem, and ciprofloxacin with median DOTs prior to CDI incidence of 14 days for the β-lactams and 26 days for ciprofloxacin. The distribution of DOT was significantly different for piperacillin/tazobactam in different units (P = 0.003) where its median DOT was the shortest in medical wards (11 days), and for ciprofloxacin among different severity groups (P = 0.013), where its median DOT was the shortest in severe CDI patients (11 days).

Conclusion
Most patients in this study had hospital-acquired non-severe CDI and were largely exposed to antibiotics and acid suppression therapy. Therefore, such therapies should be revised for necessity.