bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Endoscopic Surgical Skill Qualification on Laparoscopic Resections for Rectal Cancer in Japan: The EnSSURE Study
Authors: Ichikawa Nobuki , Homma Shigenori , Hida Koya , Akagi Tomonori , Kamada Yasuyuki , Yamaguchi Tomohiro , Ito Masaaki , Ishida Fumio , Watanabe Jun , Yamamoto Daisuke , Iijima Hiroaki , Yamaguchi Shigeki , Inomata Masafumi , Sakai Yoshiharu , Naitoh Takeshi , Taketomi Akinobu ,   EnSSURE study group collaboratives in Japan Society of Laparoscopic Colorectal Surgery
Published: April 2022

Objective:

This cohort study investigated short- and long-term postoperative outcomes of laparoscopic procedures for rectal cancer performed with versus without certified surgeons.

Background:

In Japan, the Endoscopic Surgical Skill Qualification System (ESSQS) evaluates surgical skills deemed essential for laparoscopic surgery; however, it is unknown whether this certification contributes to procedural safety.

Methods:

Outcomes of laparoscopic rectal resections for cStage II and III rectal cancer performed from 2014 to 2016 at 56 Japanese hospitals were retrospectively reviewed. The impact of having versus not having certified surgeons on postoperative complications and other short- and long-term outcomes were assessed. In cases with ESSQS-certified surgeons, surgeons attended surgery in the capacity of an operator, assistant, scope operator, or advisor.

Results:

Overall, 3188 procedures were analyzed, with 2644 procedures performed with and 544 without ESSQS-certified surgeons. A multivariate logistic regression model showed that the adjusted odds ratio of postoperative complications after procedures performed with ESSQS-certified surgeons was 0.68 (95% confidence interval, 0.51–0.91; P = 0.009). The adjusted odds ratios for conversion and pathological R0 resection rates with ESSQS-certified surgeons were 0.20 (P < 0.001) and 2.10 (P = 0.04), respectively. Multiple linear regression analyses showed significantly shorter surgical duration and more harvested lymph nodes for operations performed with ESSQS-certified surgeons. Multivariate Cox regression showed that the adjusted hazard ratios for poor overall and recurrence-free survival after operations performed with ESSQS-certified surgeons were 0.88 (P = 0.35) and 1.04 (P = 0.71), respectively.

Conclusions:

This study showed the superiority of the short-term postoperative results for laparoscopic rectal procedures performed with ESSQS-certified surgeons.
Effect of Body Mass Index on Femur Fracture Location: A Retrospective Database Study
Authors: Manirajan Aaditya , Seidel Henry , Bhattacharjee Sarah , Dillman Daryl , Shi Lewis , Strelzow Jason
Published: April 2022

Objectives:

Use a large database design and multivariable analyses to assess the associations between body mass index (BMI) and femur fracture patterns after controlling for other risk factors.

Design:

Retrospective cohort study.

Setting:

National insurance claims database of patient records from 2010 to 2018.

Patients/Participants:

Patients with femur fracture diagnoses were identified. Patients with multiple fractures within 1 week (polytrauma patients), patients without a BMI diagnosis code within 6 months of fracture, and patients with multiple BMI diagnosis codes (implying a substantial change in weight) were excluded.

Intervention:

N/A.

Main Outcome Measurements:

Patients were divided into groups based on fracture location: proximal (OTA/AO 31), shaft (OTA/AO 32), or distal (OTA/AO 33). The distribution of femur fractures was compared across BMI categories.

Results:

A total of 57,042 patients with femur fracture were identified: 45,586 proximal fractures, 4216 shaft fractures, and 7240 distal fractures. Patients with BMI <29.9 have increased odds (P < 0.0001) of proximal fracture and decreased odds (P < 0.0001) of shaft or distal fractures. Patients with BMI >30.0 have decreased odds (P < 0.0001) of proximal fracture and increased odds (P < 0.0001) of distal fractures.

Conclusions:

Increasing BMI is associated with a decreased proportion of proximal femur fractures and a corresponding increase in the proportion of shaft and distal fractures. Regression analyses determined that age, sex, osteoporosis, diabetes, and tobacco use are not the cause of this trend.

Level of Evidence:

Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Prenatal exposure to multiple organochlorine compounds and childhood body mass index
Authors: Colicino Elena , Margetaki Katerina , Valvi Damaskini , Pedretti Nicolo Foppa , Stratakis Nikos , Vafeiadi Marina , Roumeliotaki Theano , Kyrtopoulos Soterios A. , Kiviranta Hannu , Stephanou Euripides G. , Kogevinas Manolis , McConnell Rob , Berhane Kiros T. , Chatzi Leda , Conti David V.
Published: April 2022

Background:

Prenatal exposure to organochlorine compounds (OCs) has been associated with increased childhood body mass index (BMI); however, only a few studies have focused on longitudinal BMI trajectories, and none of them used multiple exposure mixture approaches.

Aim:

To determine the association between in-utero exposure to eight OCs and childhood BMI measures (BMI and BMI z-score) at 4 years and their yearly change across 4–12 years of age in 279 Rhea child-mother dyads.

Methods:

We applied three approaches: (1) linear mixed-effect regressions (LMR) to associate individual compounds with BMI measures; (2) Bayesian weighted quantile sum regressions (BWQSR) to provide an overall OC mixture association with BMI measures; and (3)Bayesian varying coefficient kernel machine regressions (BVCKMR) to model nonlinear and nonadditive associations.

Results:

In the LMR, yearly change of BMI measures was consistently associated with a quartile increase in hexachlorobenzene (HCB) (estimate [95% Confidence or Credible interval] BMI: 0.10 [0.06, 0.14]; BMI z-score: 0.02 [0.01, 0.04]). BWQSR results showed that a quartile increase in mixture concentrations was associated with yearly increase of BMI measures (BMI: 0.10 [0.01, 0.18]; BMI z-score: 0.03 [0.003, 0.06]). In the BVCKMR, a quartile increase in dichlorodiphenyldichloroethylene concentrations was associated with higher BMI measures at 4 years (BMI: 0.33 [0.24, 0.43]; BMI z-score: 0.19 [0.15, 0.24]); whereas a quartile increase in HCB and polychlorinated biphenyls (PCB)-118 levels was positively associated with BMI measures yearly change (BMI: HCB:0.10 [0.07, 0.13], PCB-118:0.08 [0.04, 012]; BMI z-score: HCB:0.03 [0.02, 0.05], PCB-118:0.02 [0.002,04]). BVCKMR suggested that PCBs had nonlinear relationships with BMI measures, and HCB interacted with other compounds.

Conclusions:

All analyses consistently demonstrated detrimental associations between prenatal OC exposures and childhood BMI measures.
Latent Neuropsychological Profiles to Discriminate Mild Traumatic Brain Injury and Posttraumatic Stress Disorder in Active-Duty Service Members
Authors: Esopenko Carrie , de Souza Nicola L. , Jia Yuane , Parrott J. Scott , Merkley Tricia L. , Dennis Emily L. , Hillary Frank G. , Velez Carmen , Cooper Douglas B. , Kennedy Jan , Lewis Jeffrey , York Gerald , Menefee Deleene S. , McCauley Stephen R. , Bowles Amy O. , Wilde Elisabeth A. , Tate David F.
Published: April 2022

Objective:

To determine whether cognitive and psychological symptom profiles differentiate clinical diagnostic classifications (eg, history of mild traumatic brain injury [mTBI] and posttraumatic stress disorder [PTSD]) in military personnel.

Methods:

US Active-Duty Service Members (N = 209, 89% male) with a history of mTBI (n = 56), current PTSD (n = 23), combined mTBI + PTSD (n = 70), or orthopedic injury controls (n = 60) completed a neuropsychological battery assessing cognitive and psychological functioning. Latent profile analysis was performed to determine how neuropsychological outcomes of individuals clustered together. Diagnostic classifications (ie, mTBI, PTSD, mTBI + PTSD, and orthopedic injury controls) within each symptom profile were examined.

Results:

A 5-profile model had the best fit. The profiles differentiated subgroups with high (34.0%) or normal (21.5%) cognitive and psychological functioning, cognitive symptoms (19.1%), psychological symptoms (15.3%), and combined cognitive and psychological symptoms (10.0%). The symptom profiles differentiated participants as would generally be expected. Participants with PTSD were mainly represented in the psychological symptom subgroup, while orthopedic injury controls were mainly represented in the high-functioning subgroup. Further, approximately 79% of participants with comorbid mTBI and PTSD were represented in a symptomatic group (∼24% = cognitive symptoms, ∼29% = psychological symptoms, and 26% = combined cognitive/psychological symptoms). Our results also showed that approximately 70% of military personnel with a history of mTBI were represented in the high- and normal-functioning groups.

Conclusions:

These results demonstrate both overlapping and heterogeneous symptom and performance profiles in military personnel with a history of mTBI, PTSD, and/or mTBI + PTSD. The overlapping profiles may underscore why these diagnoses are often difficult to diagnose and treat, but suggest that advanced statistical models may aid in identifying profiles representing symptom and cognitive performance impairments within patient groups and enable identification of more effective treatment targets.
Traumatic Brain Injury History Among Individuals Using Mental Health and Addictions Services: A Scoping Review
Authors: Davies Julia , Dinyarian Camellia , Wheeler Anne L. , Dale Craig M. , Cleverley Kristin
Published: April 2022

Objective:

Traumatic brain injury (TBI) has been increasingly linked in population research to psychiatric problems as well as substance use and related harms, suggesting that individuals with TBI may also present more frequently to mental health and addictions (MHA) services. Little is known, however, about TBI history among MHA service users. The objectives of this review were to understand (i) the prevalence of TBI history among MHA service users; (ii) how TBI history is identified in MHA service settings; and (iii) predictors or outcomes of TBI that have been reported in MHA service users.

Methods:

A scoping review was conducted in accordance with PRISMA Scoping Review Extension guidelines. A search for relevant literature was conducted in MEDLINE, PsycINFO, SPORTDiscus, CINAHL, and Embase as well as various gray literature sources.

Results:

Twenty-eight relevant studies were identified. TBI was defined and operationalized heterogeneously between studies, and TBI history prevalence rates ranged considerably among the study samples. The included studies used varied methods to identify TBI history in MHA settings, such as clinical chart audits, single-item questions, or structured questionnaires (eg, Brain Injury Screening Questionnaire or Ohio State University TBI Identification Method). TBI history was most consistently associated with indicators of more severe substance use problems and mental health symptoms as well as increased aggression or risk to others. Studies reported less consistent findings regarding the relationship of TBI to physical health, cognitive impairment, functioning, risk to self, and type of psychiatric diagnosis.

Conclusion:

Screening for TBI history in MHA settings may contribute important information for risk assessment and care planning. However, to be clinically useful, assessment of TBI history will require consistent operationalization of TBI as well as use of validated screening methods.
The Association Between Payer Source and Traumatic Brain Injury Rehabilitation Outcomes: A TBI Model Systems Study
Authors: Lequerica Anthony H. , Sander Angelle M. , Pappadis Monique R. , Ketchum Jessica M. , Jaross Marissa , Kolakowsky-Hayner Stephanie , Rabinowitz Amanda , Callender Librada , Smith Michelle
Published: April 2022

Objective:

To examine the relationship between payer source for acute rehabilitation, residential median household income (MHI), and outcomes at rehabilitation discharge after traumatic brain injury (TBI).

Setting:

Acute inpatient rehabilitation facilities.

Participants:

In total, 8558 individuals enrolled in the Traumatic Brain Injury Model Systems (TBIMS) National Database who were admitted to inpatient rehabilitation between 2006 and 2019 and were younger than 64 years.

Design:

Secondary data analysis from a multicenter longitudinal cohort study.

Main Measures:

Payer source was divided into 4 categories: uninsured, public insurance, private insurance, and workers' compensation/auto. Relationships between payer source with residential MHI, rehabilitation length of stay (RLOS), and the FIM Instrument at discharge were examined. Covariates included age, injury severity, FIM at admission, and a number of sociodemographic characteristics including minority status, preinjury limitations, education level, and employment status.

Results:

Individuals with workers' compensation/auto or private insurance had longer RLOS than uninsured individuals or those with public insurance after controlling for demographics and injury characteristics. An adjusted model controlling for demographics and injury characteristics showed a significant main effect of payer source on FIM scores at discharge, with the highest scores noted among those with workers' compensation/auto insurance. The main effect of payer source on FIM at discharge became nonsignificant after RLOS was added to the model as a covariate, suggesting a mediating effect of RLOS.

Conclusion:

Payer source was associated with preinjury residential MHI and predicted RLOS. While prior studies have demonstrated the effect of payer source on long-term outcomes due to lack of inpatient rehabilitation or quality follow-up care, this study demonstrated that individuals with TBI who are uninsured or have public insurance may be at risk for poorer functional status at the point of rehabilitation discharge than those with private insurance, particularly compared with those with workers' compensation/auto insurance. This effect may be largely driven by having a shorter length of stay in acute rehabilitation.
Clinicopathological features and management of colonic lipomas
Authors: Erginoz Ergin , Uludag Server Sezgin , Cavus Gokce Hande , Zengin Kagan , Ozcelik Mehmet Faik
Published: April 2022

Introduction:

Colonic lipomas are benign tumors of adipose tissue that are often asymptomatic, but they may present with rectal bleeding or obstructive symptoms. These tumors are unique in that they are rarely encountered within the gastrointestinal system and can mimic malignant tumors in appearance. Surgical resection and endoscopic removal of tumors have been shown to be successful in their management.

Patient concerns:

In this report, we present 3 cases of colonic lipomas, 2 of which are located in the cecum and the other within the sigmoid colon. The presenting symptoms of the patients included abdominal pain, constipation, and dyspepsia.

Diagnosis:

Patients typically presented with anemia and an elevated C-reactive protein count. Colonoscopic and computerized tomography findings were used for diagnosis.

Interventions:

Hemicolectomy was performed, depending on the localization, and the pathologic specimens were consistent with lipoma.

Outcomes:

Surgical resection was curative in all patients. The postoperative period was uneventful in all patients and all patients are symptom-free and alive at 3 years follow-up.

Conclusion:

Colonic lipomas are benign mesenchymal tumors of the gastrointestinal system with a male predominance and are observed within the fourth to sixth decades of life. Various genetic abnormalities have been reported and they have been linked to the formation of intussusception. The squeeze sign on radiological imaging, cushion sign and tenting sign in colonoscopy, and naked fat sign during pathologic examination is helpful towards reaching a diagnosis. Surgical resection is the treatment of choice but minimally invasive endoscopic approaches have also been shown to be successful.
Minimally invasive pedicle screw fixation, including the fractured vertebra, combined with percutaneous vertebroplasty for treatment of acute thoracolumbar osteoporotic compression fracture in middle-age and elderly individuals
Authors: Liu Hong , Xu Jin-wei , Sun Guan-Rong , Shi Wei-Feng , Xiang Li-Ming , Chen Shan
Published: April 2022

To evaluate the feasibility, efficacy, and safety of minimally invasive pedicle screw (MIPS) fixation, including the fractured vertebra, combined with percutaneous vertebroplasty (PVP) for the treatment of acute thoracolumbar osteoporotic compression fracture in middle-age and elderly individuals.

Between January 2016 and August 2019, a total of 30 patients, with a mean age of 69.4 years (range, 58–75 years), who experienced thoracic or lumbar fracture without neurological deficits, underwent the MIPS procedure combined with PVP. Preoperative and postoperative pain were assessed using a visual analog scale and Oswestry Disability Index. Cobb angles and anterior column height were measured on lateral radiographs before surgery and at 3 days, 1, 3, and 6 months, and 1 and 2 years at final follow-up after surgery.

All patients underwent surgery successfully, with a mean follow-up of 18.2 ± 5.7 months (range, 12–45 months). Mean preoperative visual analog scale score decreased from 7.3 ± 2.2 to 1.4 ± 0.3 at the final follow-up (P < .05). Mean preoperative Oswestry Disability Index decreased from 84.2 ± 10.3 to 18.8 ± 7.5 (P < .05) at the final follow-up. The Kyphosis angle of operative segment was improved from preoperative (21.38 ± 1.68)° to (4.01 ± 1.38)° 3 days postoperatively and (5.02 ± 1.09)° at final follow-up (P < .05). The anterior vertebral height was improved from preoperative (49.86 ± 6.50)% to (94.01 ± 1.79)% 3 days postoperatively and (91.80 ± 1.88)% at final follow-up (P < .05). No significant changes in vertebral body height restoration were observed during 2 years of follow-up after surgery. In addition, there were no instrumentation failures or complications in any of the patients.

MIPS, including the fractured vertebra, combined with PVP, was a reliable and safe procedure, with satisfactory clinical and radiological results for the treatment of thoracolumbar osteoporotic compression fracture in patients without neurological deficits.
Traumatic trigeminal neuropathy after whiplash injury
Authors: Jang Sung Ho , Seo Jeong Pyo , Kwon Young Hyeon
Published: April 2022

Rationale:

Many studies using diffusion tensor tractography (DTT) have reported trigeminal neuropathy in various neurological diseases. However, no study on traumatic trigeminal neuropathy following whiplash has been reported.

Patient concerns:

A 51-year old female suffered an indirect head trauma resulting from a flexion-hyperextension injury. At approximately 30 minutes after onset, she began to sense a headache in the left frontal area and sensory changes in the left facial area, signs that intensified with the passage of time. At 7 days after onset, she visited the rehabilitation department of our university hospital and described the characteristics and severity of pain as follows: headache on the left frontal area including the forehead with intermittent squeezing and numbness sensations. Her visual analog scale pain score was 6 with her left cheek having a continuous, dull, swelling sensation (visual analog scale score: 1). On neurological examination, she revealed mild allodynia without hyperalgesia or somatosensory change on the head, cheek, tongue, and oral cavity.

Diagnosis:

Diffusion tensor imaging data were acquired 7 days after onset. On DTT, the left trigeminal nerve showed discontinuation in the middle portion compared to that of the right trigeminal nerve. Traumatic trigeminal neuropathy was diagnosed based on her clinical features and DTT findings.

Intervention:

She was prescribed carbamazepine (200 mg/day) and pregabalin (150 mg/day), and her facial pain was well-controlled to a tolerable level.

Outcomes:

These drugs were stopped after approximately 7 month's administration, however, she did not complain of facial pain.

Lessons:

By using DTT, we demonstrated traumatic trigeminal neuropathy in a patient with whiplash. We suggest that DTT would be a useful tool for detection of traumatic trigeminal neuropathy in patients who show clinical features of trigeminal neuropathy following whiplash.
Challenges of senior 8-year-program medical students’ scientific research in China
Authors: Wan Mengyao , Liu Shuang , Zhu Jiawei , Xiao Sulong , Yuan Lei , Lei Xiaokang , Lei Hao , Shi Xiaomin , You Wen , Ruan Gechong , Li Ji
Published: April 2022

Among the diverse medical education systems in China, the 8-year program is dedicated to cultivating physician scientists. Although the research ability of senior students in 8-year medical programs is a pivotal quality, it remains unclear. This study aimed to clarify the current status and challenges of students’ research experience, abilities, and outputs.

A multicenter cross-sectional study was conducted in 5 medical schools in northern China. Electronic questionnaires were sent to 235 randomly chosen fifth-grade or sixth-grade 8-year-program medical students. A total of 211 responses were collected and analyzed using SPSS 22.0.

Only 13.3% of participants chose research as their future career goal. Students generally felt that conducting research was stressful and difficult. The greatest obstacle was a lack of time due to heavy workloads. The 2 major motivations for research were graduation and/or future employment (75.8%) and research interest (24.2%). More than half of the students (142, 67.3%) had research experience by the time of the survey, among whom 84 students already had research outputs. A higher proportion of students with outputs was motivated by the requirements for graduation or employment compared to students without outputs (71.4% vs 55.2%, P 
= 
.046).

Senior 8-year-program medical students in China generally had high pressure to conduct research and devoted their efforts to overcome these challenges. More guidance and novel encouragement to enhance students’ initiative and interest in research could be provided by medical schools and educators in the future.
Septic cavernous sinus thrombosis after minor head trauma
Authors: Kim Jae-Myung , Kang Kyung Wook , Kim Hyunsoo , Lee Seung-Han , Kim Tae-Sun , Park Man-Seok
Published: April 2022

Rationale:

Septic cavernous sinus thrombosis (SCST) is a rare but life-threatening condition that commonly arises from infections, including paranasal sinusitis, otitis media, and skin infection. Meanwhile, head trauma as a predisposing factor of SCST has been scarcely reported. We report a case of SCST complicated by meningitis after minor head trauma, even in the absence of identifiable fractures.

Patient concerns and diagnosis:

A 77-year-old female presented with diplopia combined with ocular pain and headache lasting a week. She had a recent blunt head trauma 2 weeks before the diplopia onset. The trauma was not accompanied by identifiable skull fractures, bleeding, or loss of consciousness. Neurological examination revealed incomplete ptosis, eyelid swelling, and medial and vertical gaze limitations of both eyes. Gadolinium-enhanced brain magnetic resonance imaging demonstrated multifocal thrombotic filling defects, including those of the cavernous sinus, sinusitis involving the sphenoid and ethmoid sinuses, and otomastoiditis. The cerebrospinal fluid assay result was compatible with bacterial meningitis. A tentative diagnosis of SCST complicated by bacterial meningitis and multifocal cerebral venous thrombosis was made based on clinical, laboratory, and neuroradiologic findings.

Intervention:

Intravenous triple antibiotic therapy (vancomycin, ceftriaxone, and ampicillin) for 2 weeks combined with methylprednisolone (1 g/d for 5 days) was administered. Despite the initial treatment, carotid-cavernous fistula was newly developed during hospitalization. Therefore, coil embolization was performed successfully for the treatment of carotid-cavernous fistula.

Outcomes:

The symptoms of the patient including diplopia gradually improved during the 8-month follow-up period.

Lessons:

Minor head trauma is a rare but possible cause of SCST. Early recognition and prompt treatment are essential for improving outcomes. Moreover, close observation is warranted, even if apparent serious complications were absent during initial evaluations in minor head trauma.
Effects of Low-Frequency (0.5 Hz) and High-Frequency (10 Hz) Repetitive Transcranial Magnetic Stimulation on Neurological Function, Motor Function, and Excitability of Cortex in Ischemic Stroke Patients
Authors: Wang Chao , Zeng Qifan , Yuan Zhigang , Wang Wei , Shen Mei
Published: April 2022

Background:

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive neuromodulation technique. The purpose of our study is to explore the effects of low-frequency (0.5 Hz) and high-frequency (10 Hz) rTMS on neurological function, motor function, and excitability of cortex in Chinese ischemic stroke patients.

Materials and Methods:

A total of 240 ischemic stroke patients were collected. The National Institutes of Health Stroke Scale (NIHSS), modified Rankin Scale (mRS), motor-evoked potential (MEP) cortical latency, central motor conduction time (CMCT), Fugel-Meyer assessment (FMA), Berg balance scale (BBS), and modified Barthel index (MBI) scores were recorded.

Results:

After treatment, the NIHSS, mRS, MEP cortical latency, CMCT, FMA, BBS, and MBI scores of the high-frequency group and low-frequency group were significantly improved than the sham stimulation group, and the changes in the low-frequency group were more significant (adjusted P<0.05). Compared with the sham stimulation group, high-frequency stimulation reduced the NIHSS score by 9.5%, mRS score by 12.6%, MEP latency by 2.5%, and CMCT by 5.8%, and increased the upper limb FMA scale by 16.4%, lower limb FMA scale by 8.8%, BBS by 26.3%, and MBI by 9.3%, while low-frequency stimulation reduced the NIHSS score by 23.8%, mRS score by 25.3%, MEP Latency by 11.7%, and CMCT by 9.1%, and increased the upper limb FMA scale by 24.1%, lower limb FMA scale by 18.4%, BBS by 27.4%, and MBI by 23.7% in our cohort.

Conclusions:

Low-frequency rTMS is better than high-frequency rTMS stimulation in improving neurological function, motor function, and excitability of cortex in ischemic stroke.
18F-FDG PET/CT Appearance of Radiation-Induced Delayed Transverse Myelitis
Authors: Choudhury Sayak , Purandare Nilendu , Shah Sneha , Agrawal Archi , Rangarajan Venkatesh
Published: April 2022

Delayed-onset radiation-induced myelitis is a rare but serious complication of radiation exposure to the spinal cord. In this report, we describe the 18F-FDG PET/CT findings of radiation-induced myelitis in a patient with carcinoma of buccal mucosa treated with external beam radiotherapy.
Clostridium weizhouense sp. nov., an anaerobic bacterium isolated from activated sludge of petroleum wastewater
Authors: Li Qing , Shen Taiming , Dong Yingying , Liu Yuhui , Nong Jieliang , Pan Jiayuan , Fu Bei , Xie Qinglin
Published: April 2022

A Gram-stain-positive, anaerobic, spore-forming, rod-shaped (0.4–0.6 µm×2.5–3.2 µm), flagellated bacterium, designated strain YB-6T, was isolated from activated sludge of an anaerobic tank at Weizhou marine oil mining wastewater treatment plant in Beihai, Guangxi, PR China. The culture conditions were 25–45 °C (optimum, 37 °C), pH 4–12 (pH 7.0) and NaCl concentration of 0–7 % w/v (0%). Strain YB-6T grew slowly in petroleum wastewater and removed 68.2 % of the total organic carbon in petroleum wastewater within 10 days. Concentrations of naphthalene, anthracene and phenanthrene at an initial concentration of 50 mg l−1 were reduced by 32.8, 40.4 and 14.6 %, respectively, after 7 days. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YB-6T belongs to

Clostridium

cluster I and is most closely related to

Clostridium uliginosum

CK55T (98.5 % similarity). The genome size of strain YB-6T was 3.96 Mb, and the G+C content was 26.5 mol%. The average nucleotide identity value between strain YB-6T and

C. uliginosum

CK55T was 81.9 %. The major fatty acids in strain YB-6T were C14 : 0 FAME, C16 : 0 FAME and summed feature 4 (unknown 14.762 and/or C15 : 2 FAME). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, one unidentified glycolipid and one unidentified aminolipid. Diaminopimelic acid was not detected in the strain YB-6T cell walls. Whole-cell sugars mainly consisted of ribose and galactose. Based on the results of phenotypic and genotypic analyses, strain YB-6T represents a novel species of the genus

Clostridium

, for which the name Clostridium weizhouense sp. nov. is proposed. The type strain is YB-6T (=GDMCC 1.2529T=JCM 34754T).
Microbial–stem cell interactions in periodontal disease
Authors: Iliopoulos Jordan M. , Layrolle Pierre , Apatzidou Danae A.
Published: April 2022

Periodontitis is initiated by hyper-inflammatory responses in the periodontal tissues that generate dysbiotic ecological changes within the microbial communities. As a result, supportive tissues of the tooth are damaged and periodontal attachment is lost. Gingival recession, formation of periodontal pockets with the presence of bleeding, and often suppuration and/or tooth mobility are evident upon clinical examination. These changes may ultimately lead to tooth loss. Mesenchymal stem cells (MSCs) are implicated in controlling periodontal disease progression and have been shown to play a key role in periodontal tissue homeostasis and regeneration. Evidence shows that MSCs interact with subgingival microorganisms and their by-products and modulate the activity of immune cells by either paracrine mechanisms or direct cell-to-cell contact. The aim of this review is to reveal the interactions that take place between microbes and in particular periodontal pathogens and MSCs in order to understand the factors and mechanisms that modulate the regenerative capacity of periodontal tissues and the ability of the host to defend against putative pathogens. The clinical implications of these interactions in terms of anti-inflammatory and paracrine responses of MSCs, anti-microbial properties and alterations in function including their regenerative potential are critically discussed based on literature findings. In addition, future directions to design periodontal research models and study ex vivo the microbial–stem cell interactions are introduced.
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina
Authors: Malar C Mathu , Wang Yan , Stajich Jason E. , Kokkoris Vasilis , Villeneuve-Laroche Matthew , Yildirir Gokalp , Corradi Nicolas
Published: April 2022

The arbuscular mycorrhizal fungi (AMFs) are obligate root symbionts in the subphylum Glomeromycotina that can benefit land plants by increasing their soil nutrient uptake in exchange for photosynthetically fixed carbon sources. To date, annotated genome data from representatives of the AMF orders Glomerales, Diversisporales and Archaeosporales have shown that these organisms have large and highly repeated genomes, and no genes to produce sugars and fatty acids. This led to the hypothesis that the most recent common ancestor (MRCA) of Glomeromycotina was fully dependent on plants for nutrition. Here, we aimed to further test this hypothesis by obtaining annotated genome data from a member of the early diverging order Paraglomerales (Paraglomus occultum). Genome analyses showed this species carries a 39.6 Mb genome and considerably fewer genes and repeats compared to most AMF relatives with annotated genomes. Consistent with phylogenies based on ribosomal genes, our phylogenetic analyses suggest P. occultum as the earliest diverged branch within Glomeromycotina. Overall, our analyses support the view that the MRCA of Glomeromycotina carried hallmarks of obligate plant biotrophy. The small genome size and content of P. occultum could either reflect adaptive reductive processes affecting some early AMF lineages, or indicate that the high gene and repeat family diversity thought to drive AMF adaptability to host and environmental change was not an ancestral feature of these prominent plant symbionts.
Characterization of CRISPR-Cas systems in Bifidobacterium breve
Authors: Han Xiao , Zhou Xingya , Pei Zhangming , Stanton Catherine , Ross R. Paul , Zhao Jianxin , Zhang Hao , Yang Bo , Chen Wei
Published: April 2022

The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in

Bifidobacterium breve

, the occurrence and diversity of CRISPR-Cas systems were analysed in 150

B. breve

strains. Specifically, 47 % (71/150) of

B. breve

genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in

B. breve

can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in

B. breve

, and the protospacer adjacent motif sequences were further characterized in

B. breve

type I-C system as 5′-TTC-3′. All these results might provide a molecular basis for the development of endogenous genome editing tools in

B. breve

.
Prophage-mediated genome differentiation of the Salmonella Derby ST71 population
Authors: Yu Jinyan , Xu Xiaomeng , Wang Yu , Zhai Xianyue , Pan Zhiming , Jiao Xinan , Zhang Yunzeng
Published: April 2022

Although

Salmonella

Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known

Salmonella

pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of

Salmonella

.
High neutralizing activity against Omicron BA.2 can be induced by COVID-19 mRNA booster vaccination
Authors: Tjan Lidya Handayani , Furukawa Koichi , Kurahashi Yukiya , Sutandhio Silvia , Nishimura Mitsuhiro , Arii Jun , Mori Yasuko
Published: April 2022

The VOC of SARS-CoV-2, Omicron (BA.1, BA.1.1, BA.2, or BA.3), is associated with an increased risk of reinfection. BA.2 has become the next dominant variant worldwide. Although BA.2 infection has been shown to be mild illness, its high transmissibility will result in high numbers of cases. In response to the surge of Omicron BA.1 cases, booster vaccination was initiated in many countries. But there is limited evidence regarding the effectiveness of a booster vaccination against BA.2. We collected blood samples from 84 physicians at Kobe University Hospital, Japan, in January 2022 ∼7 months after they had received two BNT162b2 vaccinations and ∼2 weeks after their booster vaccination. We performed a serum neutralizing assay against BA.2 using authentic virus.

Although most of the participants had no or a very low titer of neutralizing antibody against BA.2 at 7 months after two BNT162b2 vaccinations, the titer increased significantly at 2 weeks after the booster vaccination.
Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities
Authors: D’Aoust Patrick M. , Tian Xin , Towhid Syeda Tasneem , Xiao Amy , Mercier Elisabeth , Hegazy Nada , Jia Jian-Jun , Wan Shen , Kabir Md Pervez , Fang Wanting , Fuzzen Meghan , Hasing Maria , Yang Minqing Ivy , Sun Jianxian , Plaza-Diaz Julio , Zhang Zhihao , Cowan Aaron , Eid Walaa , Stephenson Sean , Servos Mark R. , Wade Matthew J. , MacKenzie Alex E. , Peng Hui , Edwards Elizabeth A. , Pang Xiao-Li , Alm Eric J. , Graber Tyson E. , Delatolla Robert
Published: April 2022

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the extant and anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) is likely to have greater value as an important diagnostic tool to inform public health. As the widespread adoption of WWS is relatively new at the scale employed for COVID-19, interpretation of data, including the relationship to clinical cases, has yet to be standardized. An in-depth analysis of the metrics derived from WWS is required for public health units/agencies to interpret and utilize WWS-acquired data effectively and efficiently. In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven different cities in Canada over periods ranging from 8 to 21 months. Significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing in these communities. The WC ratio decreased significantly during the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community’s wastewater (40-60% allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community’s wastewater (40-60% allelic proportion). Finally, a rapid and significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant’s greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when vaccine-induced community immunity was high. The WC ratio, used as an additional monitoring metric, complements clinical case counts and wastewater signals as individual metrics in its ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.
pH as an eco-evolutionary driver of priority effects
Authors: Chappell Callie R. , Dhami Manpreet K. , Bitter Mark C. , Czech Lucas , Paredes Sur Herrera , Eritano Katherine , Golden Lexi-Ann , Hsu Veronica , Kieschnick Clara , Rush Nicole , Fukami Tadashi
Published: April 2022

Priority effects, where arrival order and initial relative abundance modulate local species interactions, can exert taxonomic, functional, and evolutionary influences on ecological communities by driving them to alternative states. It remains unclear if these wide-ranging consequences of priority effects can be explained systematically by a common underlying factor. Here, we identify such a factor in an empirical system. In a series of field and laboratory studies, we focus on how pH affects nectar-colonizing microbes and their interactions with plants and pollinators. In a field survey, we found that nectar microbial communities in a hummingbird-pollinated shrub, Diplacus aurantiacus, exhibited patterns indicative of alternative stable states through domination by either bacteria or yeasts within individual flowers. In laboratory experiments, Acinetobacter nectaris, the bacterium most commonly found in D. aurantiacus nectar, exerted a strongly negative priority effect against Metschnikowia reukaufii, the most common nectar-specialist yeast, by reducing nectar pH. This priority effect likely explains the mutually exclusive pattern of dominance found in the field survey. Furthermore, experimental evolution simulating hummingbird-assisted dispersal between flowers revealed that M. reukaufii could evolve rapidly to improve resistance against the priority effect if constantly exposed to A. nectaris-induced pH reduction. Finally, in a field experiment, we found that low nectar pH could reduce nectar consumption by hummingbirds, suggesting functional consequences of the pH-driven priority effect for plant reproduction. Taken together, these results show that it is possible to identify an overarching factor that governs the eco-evolutionary dynamics of priority effects across multiple levels of biological organization.
SUMOylation controls the rapid transcriptional reprogramming induced by anthracyclines in Acute Myeloid Leukemias
Authors: Boulanger Mathias , Kifagi Chamseddine , Ristic Marko , Gabellier Ludovic , Tempé Denis , Sigurdsson Jon-Otti , Kaoma Tony , Andrieu-Soler Charlotte , Forné Thierry , Soler Eric , Hicheri Yosr , Gueret Elise , Vallar Laurent , Olsen Jesper V , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume
Published: April 2022

Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR), one of the main drugs used to treat Acute Myeloid Leukemia (AML), induces broad transcriptional changes in AML cells before cell death induction. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, which limits both the positive and negative effects of DNR on transcription. Quantitative proteomics shows that proteins that are deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. Its induction is preceded by a SUMO-dependent reconfiguration of chromatin loops engaging its CTCF- and SUMO-bound promoter with distal cis-regulatory regions. Altogether, our work suggests that one of the earliest effects of DNR in AML cells is a SUMO-dependent transcriptional reprogramming.
Lagrange-NG: The next generation of Lagrange
Authors: Bettisworth Ben , Smith Stephen A. , Stamatakis Alexandros
Published: April 2022

Abstract

Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 2.5 times faster, which we call Lagrange-NG (Next Generation). We further reduce time-to-completion by introducing a multi-grained parallelization approach, achieving a total parallel speedup of 8.5 over Lagrange on a machine with 8 cores. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees in order to assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2.
Dynamics and Energetics of Bottlenose Dolphins (Tursiops truncatus) Fluke-and-Glide Gait
Authors: Zhang Ding , Wang Yifan , Gabaldon Joaquin , Lauderdale Lisa K. , Miller Lance J. , Barton Kira , Shorter Kenneth Alex
Published: April 2022

Intermittent locomotion composed of periods of active flapping/stroking followed by inactive gliding has been observed with species that inhabit both aerial and marine environments. However, studies on the energetic benefits of a fluke-and-glide (FG) gait during horizontal locomotion are limited for dolphins. This work presents a physics-based model of FG gait and analysis of the associated costs of transport of bottlenose dolphins (Tursiops truncatus). New estimates of gliding drag coefficients for the model were estimated experimentally from free-swimming bottlenose dolphins. The data-driven approach used kinematic measurement from 84 hours of biologging tag data collected from 3 animals to estimate the coefficients. A set of 532 qualified gliding events were automatically extracted for gliding drag coefficient estimation, and an additional 783 FG bouts were parameterized and used to inform the model-based dynamic analysis. Experimental results indicate that FG gait was preferred at speeds around 2.2 - 2.7 m/s. Observed FG bouts had an average duty factor of 0.45 and gliding duration of 5 sec. The average associated metabolic cost of transport (COT) and mechanical cost of transport (MECOT) of FG gait are 2.53 and 0.35 J · m−1 · kg−1 at the preferred speeds. This corresponded to an 18.9% and 27.1% reduction in cost when compared to modeled continuous fluking gait at the same reference speed. Average thrust was positively correlated with fluking frequency and amplitude as animals accelerated during the FG bouts. While fluking frequency and amplitude were negatively correlated for a given thrust range. These results support the supposition that FG gait enhances the horizontal swimming efficiency of bottlenose dolphins and provides new dynamical insights into the gait of these animals.