bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNAcycP: a deep learning tool for DNA cyclizability prediction
Authors: Li Keren , Carroll Matthew , Vafabakhsh Reza , Wang Xiaozhong A , Wang Ji-Ping 
Published: February 2022

Abstract
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.
Perspective on COVID-19 vaccination in patients with immune-mediated kidney diseases: consensus statements from the ERA-IWG and EUVAS
Authors: Stevens Kate I , Frangou Eleni , Shin Jae I l , Anders Hans-Joachim , Bruchfeld Annette , Schönermarck Ulf , Hauser Thomas , Westman Kerstin , Fernandez-Juarez Gema M , Floege Jürgen , Goumenos Dimitrios , Turkmen Kultigin , van Kooten Cees , McAdoo Stephen P , Tesar Vladimir , Segelmark Mårten , Geetha Duvuru , Jayne David R W , Kronbichler Andreas ,   Immunonephrology Working Group (IWG) of the European Renal Association (ERA) and the European Vasculitis Society (EUVAS)
Published: February 2022

ABSTRACT
Patients with immune-mediated kidney diseases are at increased risk of severe coronavirus disease 2019 (COVID-19). The international rollout of COVID-19 vaccines has provided varying degrees of protection and enabled the understanding of vaccine efficacy and safety. The immune response to COVID-19 vaccines is lower in most patients with immune-mediated kidney diseases; either related to immunosuppression or comorbidities and complications caused by the underlying disease. Humoral vaccine response, measured by the presence of antibodies, is impaired or absent in patients receiving rituximab, mycophenolate mofetil (MMF), higher doses of glucocorticoids and likely other immunosuppressants, such as cyclophosphamide. The timing between the use of these agents and administration of vaccines is associated with the level of immune response: with rituximab, vaccine response can only be expected once B cells start to recover and patients with transient discontinuation of MMF mount a humoral response more frequently. The emergence of new COVID-19 variants and waning of vaccine-induced immunity highlight the value of a booster dose and the need to develop mutant-proof vaccines. COVID-19 vaccines are safe, exhibiting a very low risk of de novo or relapsing immune-mediated kidney disease. Population-based studies will determine whether this is causal or coincidental. Such cases respond to standard management, including the use of immunosuppression. The Immunonephrology Working Group and European Vasculitis Society recommend that patients with immune-mediated kidney diseases follow national guidance on vaccination. Booster doses based on antibody measurements could be considered.
Variability in Urinary Nicotine Exposure Biomarker Levels Between Waves 1 (2013–2014) and 2 (2014–2015) in the Population Assessment of Tobacco and Health Study
Authors: Ashley David L , Zhu Wanzhe , Wang Lanqing , Sosnoff Connie , Feng Jun , Del Valle-Pinero Arseima Y , Cheng Yu-Ching , Chang Cindy M , van Bemmel Dana , Borek Nicolette , Kimmel Heather L , Silveira Marushka L , Blount Benjamin C 
Published: February 2022

AbstractIntroductionTo date, no studies have evaluated the consistency of biomarker levels in people who smoke over a long-time period in real-world conditions with a large number of subjects and included use behavior and measures of nicotine metabolism. We evaluated the variability of biomarkers of nicotine exposure over approximately a 1-year period in people who exclusively smoke cigarettes, including intensity and recency of use and brand switching to assess impact on understanding associations with product characteristics.Aims and MethodsMultivariate regression analysis of longitudinal repeated measures of urinary biomarkers of nicotine exposure from 916 adults in the Population Assessment of Tobacco and Health (PATH) Study with demographic characteristics and use behavior variables. Intraclass correlation coefficients (ICCs) were calculated to examine individual variation of nicotine biomarkers and the uncertainty of repeat measures at two time points (Waves 1 and 2).ResultsAge, race, and urinary creatinine were significant covariates of urinary cotinine. When including use behavior, recency, and intensity of use were highly significant and variance decreased to a higher extent between than within subjects. The ICC for urinary cotinine decreased from 0.7530 with no use behavior variables in the model to 0.5763 when included. Similar results were found for total nicotine equivalents.ConclusionsUrinary nicotine biomarkers in the PATH Study showed good consistency between Waves 1 and 2. Use behavior measures such as time since last smoked a cigarette and number of cigarettes smoked in the past 30 days are important to include when assessing factors that may influence biomarker concentrations.ImplicationsThe results of this study show that the consistency of the nicotine biomarkers cotinine and total nicotine equivalents in spot urine samples from Waves 1 to 2 of the PATH Study is high enough that these data are useful to evaluate the association of cigarette characteristics with biomarkers of exposure under real-world use conditions.
A phytoplasma effector acts as a ubiquitin-like mediator between floral MADS-box proteins and proteasome shuttle proteins
Authors: Kitazawa Yugo , Iwabuchi Nozomu , Maejima Kensaku , Sasano Momoka , Matsumoto Oki , Koinuma Hiroaki , Tokuda Ryosuke , Suzuki Masato , Oshima Kenro , Namba Shigetou , Yamaji Yasuyuki 
Published: February 2022

AbstractPlant pathogenic bacteria have developed effectors to manipulate host cell functions to facilitate infection. A certain number of effectors use the conserved ubiquitin–proteasome system in eukaryotic to proteolyze targets. The proteasome utilization mechanism is mainly mediated by ubiquitin interaction with target proteins destined for degradation. Phyllogens are a family of protein effectors produced by pathogenic phytoplasmas that transform flowers into leaves in diverse plants. Here, we present a noncanonical mechanism for phyllogen action that involves the proteasome and is ubiquitin-independent. Phyllogens induce proteasomal degradation of floral MADS-box transcription factors (MTFs) in the presence of RADIATION-SENSITIVE23 (RAD23) shuttle proteins, which recruit ubiquitinated proteins to the proteasome. Intracellular localization analysis revealed that phyllogen induced colocalization of MTF with RAD23. The MTF/phyllogen/RAD23 ternary protein complex was detected not only in planta but also in vitro in the absence of ubiquitin, showing that phyllogen directly mediates interaction between MTF and RAD23. A Lys-less nonubiquitinated phyllogen mutant induced degradation of MTF or a Lys-less mutant of MTF. Furthermore, the method of sequential formation of the MTF/phyllogen/RAD23 protein complex was elucidated, first by MTF/phyllogen interaction and then RAD23 recruitment. Phyllogen recognized both the evolutionarily conserved tetramerization region of MTF and the ubiquitin-associated domain of RAD23. Our findings indicate that phyllogen functionally mimics ubiquitin as a mediator between MTF and RAD23.
Mendelian and non-Mendelian genetics in model plants
Authors: Mittelsten Scheid Ortrun 
Published: February 2022

Abstract
The “Mendelian Rules” of inheritance are cornerstones of genetics, described in Mendel’s seminal publication from 1866. The experimental results and their interpretation have been discussed in numerous ways. This perspective emphasizes the contribution of Mendel’s preparations prior to his crossing experiments to the discovery of Mendelian genetics. This thoughtful experimental design, and some fortune, avoided pitfalls that could have resulted in non-Mendelian inheritance.
Physical Therapy Is an Important Component of Postpartum Care in the Fourth Trimester
Authors: Critchley Claire J C 
Published: February 2022

Abstract

Abstract
The objectives of this Perspective paper are to educate physical therapists on their important role in assessing and treating common pregnancy- and delivery-related health conditions and to advocate for their routine inclusion in postpartum care during the fourth trimester. Pelvic floor dysfunction (PFD) and diastasis recti abdominis (DRA) are 2 examples of musculoskeletal disorders associated with pregnancy and childbirth that can have negative physical, social, and psychological consequences. This paper reviews evidence from 2010 through 2021 to discuss the efficacy of physical therapist intervention in the fourth trimester for PFD and DRA. The role of physical therapy in the United States is compared with its role in other developed nations, with the intent of illustrating the potential importance of physical therapy in postpartum care. Evidence shows physical therapy is an effective, low-risk, therapeutic approach for PFD and DRA; however, physical therapists in the United States currently have a peripheral role in providing postpartum care. Lack of awareness, social stigma, and policy barriers prevent women from receiving physical therapist care. Recommendations are made regarding ways in which physical therapists can increase their involvement in the fourth trimester within their community, stimulate policy change, and promote improved postpartum care practices.

Impact
This Perspective highlights the valuable role of physical therapist assessment and treatment during the postpartum period for some common musculoskeletal conditions associated with pregnancy and delivery.
Volunteer Leadership in the American Physical Therapy Association: A Phenomenological Study of Early Career Physical Therapists
Authors: Bordenave Lori M , Tovin Melissa Moran , Blackinton Mary , Canbek Jennifer 
Published: February 2022

Abstract

Objective
Professional associations rely on the work of volunteer leaders to serve their members. Little is known about the experiences of individuals who choose to seek and participate in these volunteer roles in the American Physical Therapy Association (APTA). The purpose of this qualitative study was to understand the lived experience of early career professionals engaged in volunteer leadership in APTA.

Methods
The study used a phenomenological design to explore the experience of volunteer leadership by novice physical therapists. Physical therapists holding a volunteer leadership position in APTA and in the first 7 years of clinical practice were recruited using purposeful sampling. One-on-one semistructured interviews were conducted. Following transcription, interviews were analyzed and coded using the constant comparison method.

Results
Thirteen physical therapists participated. Eleven themes emerged: (1) internal factors that facilitated volunteerism—Passion, Internal drive, Always involved, Protect and advance the profession; (2) external forces that facilitated and sustained volunteer leadership—Professional role models, Meeting the leaders, Someone asked, Support of others; and (3) behaviors that sustained their involvement—Learning while doing, Future plans, and Encouraging others’ involvement.

Conclusions
Novice physical therapists who volunteer for leadership roles within APTA have a passion for protecting and advancing the profession that leads to their decision to volunteer. Other members including faculty and experienced leaders in the association facilitate their initial volunteerism and help to sustain their engagement. Support from employers, including time off and flexible schedules, and making plans for future involvement were crucial to their continued volunteer activity.

Impact Statement
Changing demographics and a limited understanding of volunteer leadership could leave APTA with a limited pool of leaders into the future. Understanding the reasons early career professionals volunteer in APTA can help develop more effective strategies to recruit and retain these leaders.
The OXTR rs53576 impacts moral permissibility of attempted but failed harms in populations of students and prisoners
Authors: He Linlin , Liu Jinting , Fan Yuhe , Leng Junhui , Wang Quanhe , Yang Cuimei , Zhang Rui , Guo Wenxuan , Zhang Jieting , Gong Pingyuan 
Published: February 2022

Abstract
Previous research has highlighted the roles of oxytocin in empathy and altruistic behaviors. Based on these findings, recent studies have examined the association between the oxytocin receptor gene (OXTR) and outcome-based moral judgment with sacrificial dilemmas (e.g. runaway trolley case). However, little is known about the relationships between OXTR polymorphisms and intent-based moral judgment of harms (e.g. attempted but failed harm or intentionally committed harm). This study investigated the association between the OXTR rs53576 and intent-based moral judgment in college students (N = 544) and prisoners (N = 540). Results indicated that both students and prisoners with the GG genotype of OXTR rs53576 rated attempted but failed harm as less permissible than those with the AA and AG genotypes. These findings highlight the role of the OXTR gene in intent-based moral judgment.
Cerium oxide nanoparticles attenuate the renal injury induced by cadmium chloride via improvement of the NBN and Nrf2 gene expressions in rats
Authors: Bashandy, PhD Mostafa M , Saeed Hanan E , Ahmed Walaa M S , Ibrahim Marwa A , Shehata Olfat 
Published: February 2022

AbstractBackgroundCadmium (Cd) is a highly toxic heavy metal that adversely affects both human and animal health. Chronic cadmium exposure causes serious kidney damage. The current study investigated the protective role of cerium oxide nanoparticles (CeO2NPs) against cadmium chloride (CdCl2)-induced renal injury.MethodOne hundred and twenty male albino rats were divided into 6 equal groups. Group (C): considered as control group which was given distilled water orally. Group (NC.1 and NC.5): rats were injected i.p. with nanoceria at a dose of (0.1 and 0.5 mg/kg b.wt), respectively, twice a week for 2 weeks starting at the 15th day of the study. Group (Cd): rats were received CdCl2 orally (10 mg/kg b.wt) daily for 28 days. Groups (Cd + NC.1 and Cd + NC.5): rats were given CdCl2 orally (10 mg/kg b.wt) for 28 days and CeO2NPs by i.p. injection at a dose of (0.1 and 0.5 mg/kg b.wt), respectively, twice a week for 2 weeks started at the 15th day of the experiment.ResultsThe Cd group exhibited a significant increase in the serum levels of IL-1β, KIM-1, Cys-C, and β2-MG, downregulation of the antioxidant initiator genes such as Nrf-2, and up-regulation of apoptosis markers such as nibrin gene (NBN). Urine examination showed a high level of microalbuminuria, abnormal physical, chemical, and microscopical changes in comparison with control groups.ConculsionRemarkably, posttreatment with CeO2NPs showed significant improvement in kidney histopathological picture and relieved the alterations in kidney biomarkers, inflammatory markers, urine abnormalities, and expressions of different genes as Nrf-2 and NBN.
Ionized Blood Magnesium in Sick Children: An Overlooked Electrolyte
Authors: Dabla Pradeep Kumar , Sharma Shikha , Dabas Aashima , Tyagi Vernika , Agrawal Shipra , Jhamb Urmila , Begos Dennis , Upreti Kamal , Mir Rashid 
Published: February 2022

ABSTRACT

Introduction
Magnesium is a less frequently monitored electrolyte in critically ill patients. Hypomagnesemia is associated with increased need for mechanical ventilation, mortality and prolonged ICU stay. The present study was undertaken to identify the proportion of children with abnormal magnesium levels and correlate it with disease outcome.

Methods
This observational study included children aged 1 month to 12 years hospitalized at the emergency room. Heparinized blood was collected for determination of ionized magnesium, ionized calcium, sodium, potassium and lactate using Stat Profile Prime Plus (Nova Biomedical, Waltham, MA, USA). Clinical outcomes for duration of hospitalization, and death or discharge were recorded.

Results
A total of 154 (102 males) children with median (IQR) age of 11 (4, 49.75) months were enrolled. Sixty one (39.6%) had ionized magnesium levels below 0.42 mmol/l, 63 (40.9%) had normal levels and 30 (19.4%) had hypermagnesemia (&gt;0.59 mmol/l). Hypomagnesemia was associated with hypocalcemia (p &lt; 0.001), hyponatremia (p &lt; 0.001) and hypokalemia (p &lt; 0.02). A higher proportion of children with hypermagnesemia required ventilation than hypomagnesemia (26% vs. 9%) and succumbed (35% vs. 20%), respectively; p &gt; 0.05. Ninety-three (60.3%) had hypocalcemia and 10 (6.5%) children had hypercalcemia. There was good correlation between ionized calcium and magnesium values (r = 0.72, p &lt; 0.001).

Conclusion
Both hypomagnesemia and hypermagnesemia were seen in critically ill children. Patients with hypomagnesemia had significantly higher proportion of other electrolyte abnormalities.
High nerve density in breast cancer is associated with poor patient outcome
Authors: Li Dong , Hu Li Na , Zheng Si Min , La Ting , Wei Li Yuan , Zhang Xiao Jun , Zhang Zhen Hua , Xing Jun , Wang Li , Li Ruo Qi , Zhu Qin , Thorne Rick F. , Feng Yu Chen , Hondermarck Hubert , Zhang Xu Dong , Li Li , Gao Jin Nan 
Published: February 2022

AbstractActive crosstalk between the nervous system and breast cancer cells has been experimentally demonstrated in vitro and in animal models. However, low frequencies of peripheral nerve presence in human breast cancers reported in previous studies (~30% of cases) potentially negate a major role of the nervous system in breast cancer development and progression. This study aimed to clarify the incidence of nerves within human breast cancers and to delineate associations with clinicopathological features. Immunohistochemical staining was conducted in formalin‐fixed paraffin‐embedded breast cancer tissue sections using antibodies against the pan‐neuronal markers protein gene product 9.5 and growth‐associated protein 43, and the sympathetic nerve‐specific marker tyrosine hydroxylase. Nerve trunks and isolated nerve fibers were quantitated. The chi‐squared test was used to determine the associations between nerve counts and clinicopathological parameters. The log‐rank test was used to compare differences in patient progression‐free survival (PFS) and overall survival (OS). The overall frequency of peripheral nerves in breast cancers was 85%, a markedly higher proportion than reported previously. Of note, most nerves present in breast cancers were of the sympathetic origin. While high density of nerve trunks or isolated nerve fibers was associated with poor PFS and OS of patients, high nerve trunk density appeared also to predict poor patient PFS independently of lymph node metastasis. Innervation of breast cancers is a common event correlated with poor patient outcomes. These findings support the notion that the nervous system plays an active role in breast cancer pathogenesis.
New Treatment for Polycythemia Vera
Authors: Aschenbrenner Diane S. 
Published: February 2022

Ropeginterferon alfa-2b-njft (Besremi) is the first interferon for treating polycythemia vera and the first approved medication for this condition that can be taken regardless of the patient's treatment history. It is administered subcutaneously every two weeks.Like other interferon alfa products, ropeginterferon alfa-2b-njft has a boxed warning that it can cause or aggravate neuropsychiatric, autoimmune, ischemic, and infectious disorders, which can be life-threatening or fatal. Nurses should closely monitor patients for any persistently severe or worsening signs or symptoms of these adverse effects.
Hold the Antibiotics: Are Preoperative Antibiotics Unnecessary in the Treatment of Pediatric Supracondylar Humerus Fractures?
Authors: Bloomer Ainsley K. , Coe Kelsie M. , Brandt Aaron M. , Roomian Tamar , Brighton Brian , Scannell Brian P. 
Published: February 2022

Background:
Supracondylar humerus (SCH) fracture is the most common elbow injury in children and often treated with closed reduction and percutaneous pinning (CRPP). There is little published evidence supporting or refuting the use of perioperative prophylactic antibiotics for SCH CRPP in the pediatric population. The purpose of this study is to evaluate the rate of surgical site infection for patients with and without preoperative antibiotics.

Methods:
A retrospective chart review was conducted of patients less than or equal to 16 years from 2012 to 2018 who underwent primary CRPP. Open fractures, multilimbed polytraumas, and immunodeficient patients were excluded. Infection rates were compared using a noninferiority test assuming a 3% infection rate and a predefined noninferiority margin of 4%. A total of 255 patients were needed to adequately power the study.

Results:
Of the 1253 cases identified, 845 met eligibility criteria. A total of 337 received antibiotics, and 508 did not. Preoperative nerve injury (P=0.0244) and sterilization technique (P<0.0001) were associated with antibiotic use: 4 patients developed an infection; there were successfully treated superficial infections, and 1 was a deep infection requiring a formal debridement. There were 8 patients that had a recorded mal-union, and 6 patients required additional procedures; 1 patient had a postoperative compartment syndrome on postoperation day 1. The infection rates among patients treated with and without antibiotics were 0.60% and 0.40%, respectively. The absence of antibiotics was not clinically inferior to using antibiotics (P=0.003).

Conclusions:
Infection remains a rare complication following CRPP of SCH fractures. According to our current data, not giving perioperative antibiotics was not inferior to using perioperative antibiotics for preventing superficial or deep infection in patients undergoing CRPP of SCH fractures. With the increase in attention to antibiotic stewardship, it is important to eliminate unnecessary antibiotic use while continuing to maintain a low rate of surgical site infection.

Level of Evidence:
Level IV—case series. This is a therapeutic study that investigates the results from a case series.