bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designed architectural proteins that tune DNA looping in bacteria
Authors: Tse David H , Becker Nicole A , Young Robert T , Olson Wilma K , Peters Justin P , Schwab Tanya L , Clark Karl J , Maher L James 
Published: September 2021

AbstractArchitectural proteins alter the shape of DNA. Some distort the double helix by introducing sharp kinks. This can serve to relieve strain in tightly-bent DNA structures. Here, we design and test artificial architectural proteins based on a sequence-specific Transcription Activator-like Effector (TALE) protein, either alone or fused to a eukaryotic high mobility group B (HMGB) DNA-bending domain. We hypothesized that TALE protein binding would stiffen DNA to bending and twisting, acting as an architectural protein that antagonizes the formation of small DNA loops. In contrast, fusion to an HMGB domain was hypothesized to generate a targeted DNA-bending architectural protein that facilitates DNA looping. We provide evidence from Escherichia coli Lac repressor gene regulatory loops supporting these hypotheses in living bacteria. Both data fitting to a thermodynamic DNA looping model and sophisticated molecular modeling support the interpretation of these results. We find that TALE protein binding inhibits looping by stiffening DNA to bending and twisting, while the Nhp6A domain enhances looping by bending DNA without introducing twisting flexibility. Our work illustrates artificial approaches to sculpt DNA geometry with functional consequences. Similar approaches may be applicable to tune the stability of small DNA loops in eukaryotes.
COVID-19 and Co-infection in Children: The Indian Perspectives
Authors: Raychaudhuri Dibyendu , Sarkar Mihir , Roy Aniket , Roy Debapriya , Datta Kalpana , Sengupta Tapti , Hazra Avijit , Mondal Rakesh 
Published: September 2021

Abstract

Background and objectives
Assessing the co-infections with COVID-19 is crucial to delineate its true clinical impact. Pediatric information in this aspect is limited. Our study aims to analyze the spectrum of co-infections in pediatric COVID-19 patients and determine the clinical as well as laboratory parameters predicting co-infection.

Methodology
In this prospective observational study conducted from June to December 2020 in a single tertiary care institution, data pertaining to demographic, illness and treatment-related variables were analyzed among two subsets of pediatric patients of age 1 month–12 years with RT–PCR-confirmed COVID-19 infection-Group A: those with confirmed co-infection and Group B: moderate to severe disease without co-infection. Among Group A, etiology of co-infection was characterized through relevant microbiological examination within 48 h admission.

Result
Among our study population, 15.03% and 20.6% had co-infections and moderate to severe disease respectively. Among those with confirmed co-infection, 32.5%, 11.6% and 6.97% recorded blood culture, respiratory secretion and CSF growth, respectively, the picture being dominated by Methicillin resistant and sensitive Staphylococcus aureus. Serum serology demonstrated Scrub typhus infection to be most prevalent. Concurrent respiratory viral infections were seen in 11.6%. Children with co-infection had significantly higher morbidity and need for supportive therapy. Predictors of co-infection were localization of infection, Neutrophil count ≥10×109, age-specific lymphopenia, CRP &gt; 100 mg/dl and hyperferritinemia.

Conclusion
Co-infections are an important factor prognosticating pediatric COVID infection. Their early detection, prompt and appropriate treatment is of paramount importance.
Teaching Baccalaureate Students Research Concepts Using Colored Candies
Authors: Gaffney Mary K. 
Published: September 2021

Abstract
A collaborative, experiential learning activity was designed to develop nursing students’ understanding of research concepts. Working in pairs, students determine if a candy company is filling bags with equal numbers of each candy color. Pairs receive 100 colored candies and instructions to obtain simple random, systematic, stratified, and cluster samples. Color counts from each sampling method are entered on a Google spreadsheet. During debriefing, students explore results, unexpected problems (e.g., inconsistent technique, missing candies), representativeness of samples (size, inclusion/exclusion criteria), and ethical conduct. Students develop knowledge to be better consumers of research and more capable advocates for high-quality nursing care.
Psychological Interventions for Parents of Youth With Chronic Pain
Authors: Lee Soeun , Dick Bruce D. , Jordan Abbie , McMurtry C. Meghan 
Published: September 2021

Objective:
Parents are integral to their youth’s chronic pain experiences, and intervening with parents may improve parent and youth functioning. Existing systematic reviews are not specific to pain or do not systematically report critical aspects to facilitate implementation of parent interventions in diverse settings. Thus, this scoping review aimed to map published parent interventions for pediatric chronic pain to summarize the participant and intervention characteristics, treatment components, methods, outcomes, feasibility, and acceptability, as well as identify gaps for future research.

Methods:
Four databases were searched (PubMed, PsycINFO, CINAHL, and Google Scholar). Studies of any design reporting psychological interventions including parents of youth (0 to 18 y) with chronic pain were included. Data on study characteristics, treatment components, effectiveness, and feasibility/acceptability were extracted.

Results:
Fifty-four studies met inclusion criteria from 9312 unique titles. The majority were nonrandomized cognitive-behavioral therapy interventions delivered individually. The degree of parent participation ranged from 17% to 100%; the average enrollment rate was 68%. Reported parent and youth outcomes were variable; 26% of studies did not include any parent-related outcomes.

Discussion:
Parent interventions may be a helpful and feasible way to support parents and youth with chronic pain. There is variability across study characteristics, treatment content/aims, parent participation, and parent/youth outcomes.
Relationship Between Vertebral Bone Marrow Edema and Early Progression of Intervertebral Disc Wedge or Narrowing After Lumbar Decompression Surgery
Authors: Nakajima Hideaki , Honjoh Kazuya , Watanabe Shuji , Kubota Arisa , Matsumine Akihiko 
Published: September 2021

Study Design.
A retrospective study.

Objectives.
The aim of this study was to review clinical and imaging features in patients with lumbar spinal canal stenosis (LSS) with and without postoperative early progression of intervertebral disc degeneration (IDD) and to identify predictive factors.

Summary of Background Data.
Progression of IDD after lumbar decompression surgery can induce low back pain and leg pain, and may require revision surgery. However, risk factors for postoperative radiological changes indicating IDD linked to development of symptoms have not been described.

Methods.
We included 564 patients with LSS without degenerative lumbar scoliosis who underwent lumbar decompression surgery without fusion. Clinical features and imaging findings were compared in cases with (group P) and without (group N) progression of IDD (intervertebral disc wedge or narrowing) at 1 year after surgery.

Results.
Of the 564 patients, 49 (8.7%) were in group P. On preoperative MRI, all patients in group P had findings of vertebral bone marrow edema (diffuse high intensity on T2-weighted images and low-intensity on T1-weighted images), compared to only 5.4% in group N. The rate of revision surgery was significantly higher in group P in 5 years’ follow-up (12.2% vs. 1.4%, P < 0.01). In group P, 44.9% of patients developed postoperative symptoms associated with postoperative radiological changes, and the frequency was higher in narrowing-type than in wedge-type cases. Vertebral bone marrow edema area and IDD grade were not predictors for postoperative early IDD progression.

Conclusion.
Careful consideration is required to determine whether lumbar decompression surgery should be performed if vertebral bone marrow edema is detected on MRI, since this is a predictor for a negative clinical outcome. If surgery is symptomati-cally urgent, careful clinical and radiological follow-up is required.

Level of Evidence: 4
Mutational burden and immune recognition of gliomas
Authors: Prost Diego , Bielle Franck , Ligon Keith L. , Touat Mehdi 
Published: September 2021

Purpose of review
Recent evidence suggests high tumor mutational burden (TMB-H) as a predictor of response to immune checkpoint blockade (ICB) in cancer. However, results in TMB-H gliomas have been inconsistent. In this article, we discuss the main pathways leading to TMB-H in glioma and how these might affect immunotherapy response.

Recent findings
Recent characterization of TMB-H gliomas showed that ‘post-treatment’ related to mismatch repair (MMR) deficiency is the most common mechanism leading to TMB-H in gliomas. Unexpectedly, preliminary evidence suggested that benefit with ICB is rare in this population. Contrary to expectations, ICB response was reported in a subset of TMB-H gliomas associated with constitutional MMR or polymerase epsilon (POLE) defects (e.g., constitutional biallelic MMRd deficiency). In other cancers, several trials suggest increased ICB efficacy is critically associated with increased lymphocyte infiltration at baseline which is missing in most gliomas. Further characterization of the immune microenvironment of gliomas is needed to identify biomarkers to select the patients who will benefit from ICB.

Summary
Intrinsic molecular and immunological differences between gliomas and other cancers might explain the lack of efficacy of ICB in a subset of TMB-H gliomas. Novel combinations and biomarkers are awaited to improve immunotherapy response in these cancers.
A nomogram integrating non-ECG factors with ECG to screen left ventricular hypertrophy among hypertensive patients from northern China
Authors: Li Guangxiao , Shi Chuning , Li Tan , Ouyang Nanxiang , Guo XiaoFan , Chen Yanli , Li Zhao , Zhou Ying , Yang Hongmei , Yu Shasha , Sun Guozhe , Sun Yingxian 
Published: September 2021

Objective:
We aimed to establish and validate a user-friendly and clinically practical nomogram for estimating the probability of echocardiographic left ventricular hypertrophy (echo-LVH) indexed to BSA among hypertensive patients from northern China.

Methods:
A total of 4954 hypertensive patients were recruited from a population-based cohort study from January 2012 to August 2013. The dataset was randomly split into two sets: training (n = 3303) and validation (n = 1651). Three nomograms were initially constructed. That is the Cornell product nomogram, the non-ECG nomogram, and the integrated nomogram which integrated non-ECG risk factors and Cornell-voltage duration product. The least absolute shrinkage and selection operator strategies were employed to screen for non-ECG features. The performance of the nomograms was evaluated using discrimination, calibration, and decision curve analysis (DCA). The net reclassification improvement (NRI) and integrated discrimination improvement (IDI) were also calculated.

Results:
The AUCs, NRIs, IDIs, and DCA curves of the nomograms demonstrated that the integrated nomogram performed best among all three nomograms. The integrated nomogram incorporated age, sex, educational level, hypertension duration, SBP, DBP, eGFR, sleep duration, tea consumption, and the Cornell-voltage duration product. The AUC was 0.758 and had a good calibration (Hosmer–Lemeshow test, P = 0.73). Internal validation showed an acceptable AUC of 0.735 and good calibration was preserved (Hosmer–Lemeshow test, P = 0.19). The integrated nomogram was clinically beneficial across a range of thresholds of 10–50%.

Conclusion:
The integrated nomogram is a convenient and reliable tool that enables early identification of hypertensive patients at high odds of LVH and can assist clinicians in their decision-making.
Evaluation of the Correction Methods Using Age and BMI for Estimating CT Organ Dose Using a Radiophotoluminescence Glass Dosimeter and a Monte Carlo-based Dose Calculator
Authors: Chang Weishan , Koba Yusuke 
Published: September 2021

Abstract
The size-specific dose estimates (SSDE) have been recommended to replace the volume computed tomography dose index (CTDIvol) because it takes patient size into account. On the other hand, organ dose is thought to be a more appropriate quantity in the radiation protection field due to its correlation with radiation risk. The web-based computed tomography (CT) dose calculator WAZA-ARIv2 only offers organ doses for adults with four different body shapes and for children with five different ages. Since the American Association of Physicists in Medicine (AAPM) offers the conversion factors for SSDE and the correlation of SSDE with organ dose has been demonstrated, implementation of the conversion table might improve the accuracy of WAZA-ARIv2. This study aimed to evaluate a body mass index (BMI)-based and age-based correction method for estimation of the organ dose by using a radiophotoluminescence dosimeter (RGD), an anthropomorphic phantom, and the dose calculator WAZA-ARIv2. RGDs were individually calibrated by using an ISOVOLT TITAN-320 x-ray generator. The ratio of the SSDE conversion factors (CFSSDE) was used as the comparison index. For the BMI-based correction method, the ratio of CFSSDE values for the adult phantoms was expected to be 1.065, and the average ratio of the organ doses for the adult phantoms was 1.163 ± 0.169. For the age-based correction method, the ratio of CFSSDE value for 5- and 10-y-old pediatric phantoms was expected to be 0.889, and the ratios of the organ doses were 0.866 ± 0.024 and 0.909 ± 0.047 for the WAZA-ARIv2 dosimetry system and RGD dosimetry system, respectively. In conclusion, both evaluations of the experimental results showed the consistency between WAZA-ARIv2 and the SSDE conversion factor table. Moreover, the importance of taking the measurement position into account when applying the mass attenuation coefficient was demonstrated according to this study.
Mucosal defense: gastroduodenal injury and repair mechanisms
Authors: Hagen Susan J. 
Published: September 2021

Purpose of review
The mucosal barrier serves as a primary interface between the environment and host. In daily life, superficial injury to the gastric or duodenal mucosa occurs regularly but heals rapidly by a process called ‘restitution’. Persistent injury to the gastroduodenal mucosa also occurs but initiates a regenerative lesion with specific wound healing mechanisms that attempt to repair barrier function. If not healed, these lesions can be the site of neoplasia development in a chronic inflammatory setting. This review summarizes the past year of advances in understanding mucosal repair in the gastroduodenal mucosa, which occurs as a defense mechanism against injury.

Recent findings
Organoids are an emerging new tool that allows for the correlation of in vivo and in vitro models; organoids represent an important reductionist model to probe specific aspects of injury and repair mechanisms that are limited to epithelial cells. Additionally, proof-of-concept studies show that machine learning algorithms may ultimately assist with identifying novel, targetable pathways to pursue in therapeutic interventions. Gut-on-chip technology and single cell RNA-sequencing contributed to new understanding of gastroduodenal regenerative lesions after injury by identifying networks and interactions that are involved in the repair process.

Summary
Recent updates provide new possibilities for identifying novel molecular targets for the treatment of acute and superficial mucosal injury, mucosal regeneration, and regenerative lesions in the gastrointestinal tract.
Beyond Disease Intervention: Exploring an Expanded Role for Partner Services in the MATRix-NC Demonstration Project
Authors: Hurt Christopher B. , Morrison Arianne S. , Guy Jalila , Mobley Victoria L. , Dennis Ann M. , Barrington Clare , Samoff Erika , Hightow-Weidman Lisa B. , McNeil Candice J. , Carry Monique G. , Hogben Matthew , Seña Arlene C. 
Published: September 2021

Background
Disease intervention specialists (DIS) provide partner services for sexually transmitted infections (STIs). We assessed an expansion of DIS services for clients with HIV and/or syphilis, and contacts within their social and sexual networks.

Methods
Black and Latinx cisgender men and transgender women who have sex with men diagnosed with HIV and/or syphilis in 4 urban North Carolina counties were referred to designated DIS, who were trained to recruit clients as “seeds” for chain-referral sampling of sociosexual network “peers.” All received HIV/STI testing and care; referrals for preexposure prophylaxis (PrEP) and social, behavioral, and non-STI medical services were offered. Participants completed baseline, 1-month, and 3-month computerized surveys.

Results
Of 213 cases referred to DIS from May 2018 to February 2020, 42 seeds (25 with syphilis, 17 with HIV) and 50 peers participated. Median age was 27 years; 93% were Black and 86% were cisgender men. Most peers came from seeds’ social networks: 66% were friends, 20% were relatives, and 38% were cisgender women. Incomes were low, 41% were uninsured, and 10% experienced recent homelessness. More seeds than peers had baseline PrEP awareness; attitudes were favorable, but utilization was poor. Thirty-seven participants were referred for PrEP 50 times; 17 (46%) accessed PrEP by month 3. Thirty-nine participants received 129 non-PrEP referrals, most commonly for housing assistance, primary care, Medicaid navigation, and food insecurity.

Conclusions
Chain-referral sampling from partner services clients allowed DIS to access persons with significant medical and social service needs, demonstrating that DIS can support marginalized communities beyond STI intervention.
Sexual Risk Behaviors Among Persons Diagnosed With Primary and Secondary Syphilis Who Reported High-Risk Substance Use: Data From the National Notifiable Diseases Surveillance System, 2018
Authors: Copen Casey E. , Brookmeyer Kathryn A. , Haderxhanaj Laura T. , Hogben Matthew , Torrone Elizabeth A. 
Published: September 2021

Background
Recent increases in high-risk substance use (HRSU; i.e., injection drug use, heroin, methamphetamine, crack/cocaine) have coincided with rising primary and secondary (P&S) syphilis rates. To further understand these trends, we examined sexual risk behaviors among women, men who have sex with women only (MSW), and men who have sex with men (MSM) who were diagnosed with P&S syphilis in 2018 and reported HRSU.

Methods
Data on HRSU and sexual risk behaviors among persons with P&S syphilis were drawn from syphilis case reports in 2018 from the National Notifiable Diseases Surveillance System. Persons with P&S syphilis were asked about sexual risk behaviors in the past 12 months including exchange sex for drugs/money, sex while intoxicated and/or high on drugs, sex with a person who injects drugs (PWID), sex with an anonymous partner, and number of sex partners. We describe percentages and adjusted prevalence ratios (aPRs) for women, MSW, and MSM reporting these behaviors by age, race/Hispanic ethnicity, type of drug used, and incarceration history (both in the past 12 months).

Results
Among 19,634 persons diagnosed with P&S syphilis in 2018 with information on HRSU, 29.3% of women, 22.7% of MSW, and 12.4% of MSM reported HRSU. Among those reporting HRSU, percentages reporting exchange sex ranged from 17% to 35% (highest for women), whereas reports of anonymous sex ranged from 44% to 71% (highest for MSM). In this population, sexual risk behaviors were more commonly reported among those with a recent incarceration history than those without such history. Among those reporting injection drug use or heroin use, percentages reporting sex with a PWID ranged from 51% to 77%. In adjusted models, HRSU was significantly associated with one or more sexual risk behaviors for women (aPR, 2.63 [95% confidence interval {CI}, 2.39–2.90]; MSW: aPR, 1.38 [95% CI, 1.31–1.46]; and MSM: aPR, 1.30 [95% CI, 1.26–1.34]).

Conclusions
Collaborative partnerships across the US public health system could help address barriers to timely clinical care among persons diagnosed with P&S syphilis who report HRSU.
Lessons Learned From a Centers for Disease Control and Prevention Virtual Partner Services Technical Assistance Pilot Project to Respond to a Local Syphilis Outbreak
Authors: Davis Cassandra , Wright Shauntā S. , Babcock Marcie , Kingdon Elisabeth , Broussard Dawn , Oyervides Otilio , Carr Deborah 
Published: September 2021

Abstract
A virtual partner services technical assistance (TA) project was piloted with the Minnesota Department of Health to address an ongoing syphilis outbreak. The TA reduced the health department's disease intervention specialist workload, achieved partner services outcomes comparable with in-person methods, and identified lessons learned to replicate with other jurisdictions.
Antimicrobial Susceptibility of Urogenital and Extragenital Neisseria gonorrhoeae Isolates Among Men Who Have Sex With Men: Strengthening the US Response to Resistant Gonorrhea and Enhanced Gonococcal Isolate Surveillance Project, 2018 to 2019
Authors: Quilter Laura A.S. , St. Cyr Sancta B. , Hong Jaeyoung , Asbel Lenore , Bautista Ilene , Carter Bonnie , Casimir Yanick , Denny Michael , Ervin Melissa , Gomez Raquel , Harvey Alesia , Holderman Justin L. , Johnson Kimberly , Kohn Robert P. , Learner Emily R. , Mauk Kerry , Menza Timothy , Mettenbrink Christie , Nettleton William D. , Nicosia Karen R. , Pham Cau D. , Ried Christopher , Schlanger Karen , Schneider Annah , Soge Olusegun O. , Tabidze Irina , Taylor Stephanie N. , Tilghman Winston , Toler Cindy , Weinstock Hillard , Torrone Elizabeth A. 
Published: September 2021

Background
We investigated differences in gonococcal antimicrobial susceptibility by anatomic site among cisgender men who have sex with men (MSM) using specimens collected through the Centers for Disease Control and Prevention's enhanced Gonococcal Isolate Surveillance Project and Strengthening the US Response to Resistant Gonorrhea.

Methods
During the period January 1, 2018–December 31, 2019, 12 enhanced Gonococcal Isolate Surveillance Project and 8 Strengthening the US Response to Resistant Gonorrhea sites collected urogenital, pharyngeal, and rectal isolates from cisgender MSM in sexually transmitted disease clinics. Gonococcal isolates were sent to regional laboratories for antimicrobial susceptibility testing by agar dilution. To account for correlated observations, linear mixed-effects models were used to calculate geometric mean minimum inhibitory concentrations (MICs), and mixed-effects logistic regression models were used to calculate the proportion of isolates with elevated or resistant MICs; comparisons were made across anatomic sites.

Results
Participating clinics collected 3974 urethral, 1553 rectal, and 1049 pharyngeal isolates from 5456 unique cisgender MSM. There were no significant differences in the geometric mean MICs for azithromycin, ciprofloxacin, penicillin, and tetracycline by anatomic site. For cefixime and ceftriaxone, geometric mean MICs for pharyngeal isolates were higher compared with anogenital isolates (P < 0.05). The proportion of isolates with elevated ceftriaxone MICs (≥0.125 μg/mL) at the pharynx (0.67%) was higher than at rectal (0.13%) and urethral (0.18%) sites (P < 0.05).

Conclusions
Based on data collected from multijurisdictional sentinel surveillance projects, antimicrobial susceptibility patterns of Neisseria gonorrhoeae isolates may differ among MSM at extragenital sites, particularly at the pharynx. Continued investigation into gonococcal susceptibility patterns by anatomic site may be an important strategy to monitor and detect the emergence of antimicrobial resistant gonorrhea over time.