bluuebunny/crossref_metadata_2025 huggingface dataset:
Referral patterns to a pediatric orthopedic clinic: pediatric orthopedic surgeons are primary care musculoskeletal medicine physicians
Authors: Pan Tommy , Kish Alexander J. , Hennrikus William L.
Published: May 2022

In 2004, Reeder and in 2012, Schwend reported that inappropriate nonsurgical referrals to pediatric orthopedic clinics create a misuse of resources. Additional authors have called for re-emphasis and additional training in musculoskeletal medicine for primary care physicians (PCP) to improve the confidence, knowledge and performance when managing musculoskeletal conditions. The current study compares the diagnoses referred to a pediatric orthopedic clinic with diagnoses recommended for referral by the American Academy of Pediatrics (AAP) guidelines to determine if any improvement in the quality of referrals has occurred since Reeder and Schwend’s article. A chart review of new referrals to a pediatric orthopedic clinic during a 3-month-period was performed. Data were collected on age, sex, referring diagnosis, referral source, final diagnosis and treatment. In total 230 new consults were evaluated. The referral source was a PCP in 169 (73.5%) cases, 30 (13%) self-referrals by a parent, 19 (8.3%) from another orthopedic surgeon, 9 (3.9%) from a neurologist and 3 (1.3%) from another specialist. Fifty percent of referrals met the criteria outlined in the AAP guidelines for referral to a pediatric orthopedic specialist and 48% were classified as primary care musculoskeletal conditions. During the 15 years since the publication of Reeder’s study and despite a limited re-emphasis on musculoskeletal education, the percent of inappropriate referrals to a pediatric orthopedic clinic remains unchanged at 50%. We support an expanded musculoskeletal educational effort aimed at the medical, resident and pediatrician level, online decision-making aids, and implementation of a standardized referral form with the specific criteria of the AAP included.
Tracheostomy Practices and Outcomes in Patients With COVID-19 Supported by Extracorporeal Membrane Oxygenation: An Analysis of the Extracorporeal Life Support Organization Registry
Authors: Kohne Joseph G. , MacLaren Graeme , Cagino Leigh , Boonstra Philip S. , Brodie Daniel , Barbaro Ryan P.
Published: May 2022

OBJECTIVES:

The use of extracorporeal membrane oxygenation (ECMO) in patients with COVID-19 has been supported by major healthcare organizations, yet the role of specific management strategies during ECMO requires further study. We sought to characterize tracheostomy practices, complications, and outcomes in ECMO-supported patients with acute respiratory failure related to COVID-19.

DESIGN:

Retrospective cohort study.

SETTING:

ECMO centers contributing to the Extracorporeal Life Support Organization Registry.

PATIENTS:

Patients 16 years or older receiving venovenous ECMO for respiratory support for: 1) COVID-19 in 2020 and 2021 (through October 2021) and 2) pre-COVID-19 viral pneumonia in 2019.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

We identified 7,047 patients who received ECMO support for acute respiratory failure related to COVID-19. A total of 32% of patients were recorded as having a tracheostomy procedure during ECMO, and 51% had a tracheostomy at some point during hospitalization. The frequency of tracheostomy was similar in pre-COVID-19 viral pneumonia, but tracheostomies were performed 3 days earlier compared with patients with COVID-19 (median 6.7 d [interquartile range [IQR], 3.0–12.0 d] vs 10.0 d [IQR, 5.0–16.5 d]; p < 0.001). More patients were mobilized with pre-COVID-19 viral pneumonia, but receipt of a tracheostomy during ECMO was associated with increased mobilization in both cohorts. More bleeding complications occurred in patients who received a tracheostomy, with 9% of patients with COVID-19 who received a tracheostomy reported as having surgical site bleeding.

CONCLUSIONS:

Tracheostomies are performed in COVID-19 patients receiving ECMO at rates similar to practices in pre-COVID-19 viral pneumonia, although later during the course of ECMO. Receipt of a tracheostomy was associated with increased patient mobilization. Overall mortality was similar between those who did and did not receive a tracheostomy.
Impact of Pain, Agitation, and Delirium Bundle on Delirium and Cognitive Function
Authors: WANG Xiao-Ping , LV Dan , CHEN Yun-Fang , CHEN Na , LI Xiao-Dong , XU Cheng-Fei , LI Yin , TIAN Li
Published: May 2022

Background

Differences in short-term cognitive function between mechanically ventilated patients treated with multicomponent interventions and those receiving routine nursing care have not been established because of the lack of follow-up in previous studies.

Purpose

This study was designed to evaluate the effects of the pain, agitation, and delirium (PAD) care bundle on delirium occurrence and clinical outcomes, specifically in terms of short-term cognitive function, in mechanically ventilated patients.

Methods

Data on 243 patients with mechanical ventilation were analyzed from January 2017 to February 2019. The eligible patients were divided randomly into two groups. The control group (n = 120) received usual care, whereas the intervention group (n = 123) received the PAD bundle, including pain monitoring and management, light sedation and daily awakening, early mobility, sleep promotion, and delirium monitoring. The incidence and duration of delirium, ventilator time, and intensive care unit (ICU) length of stay were compared between the two groups. Upon discharge from the ICU and at 3 and 6 months after discharge, cognitive function was assessed using the Montreal Cognitive Assessment scale and compared between the two groups.

Results

The incidence of delirium was reduced significantly in the intervention group, and significant decreases in the duration of delirium, ventilator time, and ICU length of stay were found. Cognitive impairment in the intervention group was significantly lower at the 3-month follow-up assessment.

Conclusions/Implications for Practice

The PAD bundle was shown to be associated with a lower incidence of delirium and improved clinical outcomes. Short-term cognitive impairment occurred in fewer patients who were managed with the PAD bundle after ICU discharge. Our findings indicate that the PAD bundle has the potential to improve clinical outcomes. The administrative staff of ICUs should use strategies, such as interdisciplinary teamwork, to facilitate the buy-in and implementation of interventions.
Reconstruction of the thumb interphalangeal joint from the second toe proximal interphalangeal joint combined with artificial dermis covering
Authors: Wen Haihua , Deng Weicong , Hong Yongchang , Lin Zhengjiang
Published: May 2022

Rationale:

Thumb function is one of the most fundamental components of hand function, and a vast majority of hand functions are derived from thumb motion. Injury of the thumb interphalangeal joint has a tremendous impact on the function of the thumb, and damage to the thumb interphalangeal joint (IPJ) caused by trauma is usually accompanied by dislocation of the surrounding skin; therefore, it is particularly important to restore the thumb anatomy and skin coverage.

Patient concerns:

A 41-year-old woman presented with IPJ disfigurement accompanied by a local skin defect caused by machine compression of her right thumb. Restoring the appearance and function of the thumb is key to this operation.

Diagnoses:

Open fracture of the right thumb.

Interventions:

After detailed preoperative and radiographic evaluation, the appearance and function of the thumb were reconstructed by IPJ grafting and artificial dermis covering.

Outcomes:

At 4 months’ follow-up, the patient's visual analogue score was 0, no complications (eg, osteomyelitis, osteolysis, osteoarthritis, and nonunion of the artificial dermis) were observed, and the range of motion of the thumb IPJ returned to 60% of that of the healthy side.

Lessons:

The innovative application of the second toe proximal IPJ flap combined with double-layer artificial dermis covering to reconstruct the thumb IPJ defect not only solves the problem of skin defects in the recipient area after transplantation in previous cases but also restores the beauty of the recipient area, making it easier for patients to accept this surgical program.
Effectiveness of therapeutic hypothermia for mild neonatal encephalopathy
Authors: Zheng Tingting , Liu Xini , Chen Xuechun
Published: May 2022

Background:

Neonates with moderate to severe encephalopathy benefit significantly from therapeutic hypothermia, with reduced risk of death or disability. However, the need for therapeutic hypothermia for mild neonatal encephalopathy (NE) remains unclear. Therefore, we conducted a protocol for systematic review and meta-analysis to provide evidence supporting therapeutic hypothermia for term or near term neonates with mild NE, including findings of recent long-term outcome studies, as well as novel adjunctive therapies to augment neurodevelopmental outcomes for neonates with NE who receive therapeutic hypothermia.

Methods:

Two independent researchers performed a systematic literature search in different electronic databases including PubMed, the Cochrane Center Controlled Trials Register, EMBASE, Medline, Ovid, Chinese National Knowledge Infrastructure, Chinese Biomedical Literature Database, and Wanfang Database without any restrictions of languages and date. Two reviewers will screen the records and include quality studies according to inclusion criteria independently. Two reviewers will assess the risk of bias of the included studies by the “Risk of Bias Assessment Tool” of the Cochrane Handbook for randomized controlled trials. Statistical analysis will be performed with Review Manager software 5.3.

Results:

A synthesis of current evidence of therapeutic hypothermia for treating mild NE will be provided in this protocol.

Conclusion:

The results of this study will provide a theoretical basis for the clinical use of therapeutic hypothermia in mild NE.
Successful treatment of a patent urachus concurrent with pyocele in a newborn
Authors: Kang Susie , Imura Erika , Kim Yoo-Jin , Yoon Shin Ae , Lee Ji Hyuk , Park Jin-Woo
Published: May 2022

Rationale:

A patent urachus is a rare congenital anomaly that atypically presents as an umbilical cord cyst or large umbilical cord. Here we describe a case of a giant umbilical cord cyst in a newborn diagnosed as a patent urachus.

Patient concerns:

A male infant with a birth weight of 3260 g was transferred because of an antenatally diagnosed giant umbilical cord cyst accompanied by yellowish discharge and granulation in the umbilical cord after birth.

Diagnoses:

Patent urachus

Intervensions:

The patent urachus was treated by excision of the urachal remnant followed by partial cystectomy.

Outcomes:

Postoperative orchitis with pyocele occurred and was treated with a course of antimicrobial therapy; and no other complications developed.

Lessons:

Newborns with a giant umbilical cord or umbilical cord cysts should be examined for possible accompanying urachal anomalies, even if antenatal ultrasound shows no other suspicious findings, to prevent delayed diagnosis and subsequent complications.
Clinical impact of pretreatment albumin–globulin ratio in patients with colorectal cancer
Authors: Ma Jian-Ying , Liu Gang , Pan Liang-Zhi , Hu Min , Zhu Zhong-Zhong
Published: May 2022

Background:

Accumulating evidence have revealed that pretreatment albumin to globulin ratio (AGR) may be a predictor of prognosis among patients with colorectal cancer (CRC). However, these findings are inconsistent. The aim of the present study was to investigate the prognostic value of pretreatment AGR in CRC.

Methods:

A systematic meta-analysis was conducted by searching MEDLINE, EMBASE, and Cochrane Library databases.

Results:

A total of 9 studies with 7939 patients were finally included. Low pretreatment AGR was associated with worse overall survival (pooled hazard ratio [HR]: 2.07, 95% CI: 1.60–2.67, P < .001) and disease-free survival/progress-free survival (pooled hazard ratio [HR]: 2.10, 95% confidence interval [CI]: 1.34–3.31, P = .001). Subgroup analyses revealed that the pooled correlation did not alter these results. Moreover, low pretreatment AGR were associated with elderly patients, tumor diameter (≥50 mm), tumor node metastasis stage (III–IV), depth of tumor (T3–4), and CA19-9 (>37 U/mL).

Conclusion:

The present meta-analysis suggests that low pretreatment AGR was associated with advanced clinicopathological features and worse prognosis, suggesting AGR is a useful prognostic biomarker for CRC patients.
Chondroma of the urinary bladder
Authors: Kao Kuo-Wei , Cheng Weiming , Chang Yi-Chin
Published: May 2022

Rationale:

Chondromas are benign tumors comprising cartilaginous tissue that commonly occur in the small bones of the hands and feet. Chondromas are extremely rare in extraskeletal soft tissues, and only six cases of bladder chondromas have been reported thus far.

Patient concerns:

A 75-year-old woman presented with abdominal pain and urinary symptoms, including increased frequency and a weak stream.

Diagnosis:

Cystoscopy revealed a well-defined bladder mass over the anterior bladder wall. The pathology report showed neoplastic chondrocytes within the hyalinized and focal myxoid matrix, and immunopositivity for S-100, leading to the seventh known diagnosis of bladder chondroma.

Interventions:

The tumor was endoscopically resected. The postoperative stay was uneventful, and 5 days later, the patient was discharged after the removal of the urinary catheter.

Outcomes:

One month after surgery, repeated cystoscopy showed no recurrence of the bladder tumor, and the patient reported improvement in urinary symptoms and relief of lower abdominal pain.

Lessons:

Chondromas of the urinary bladder can present as urinary symptoms and abdominal pain in older patients. Transurethral resection is the treatment of choice.
Development and validation of a nomogram for preoperative prediction of lymph node metastasis in pathological T1 esophageal squamous cell carcinoma
Authors: Chen Ling , Peng Kaiming , Han Ziyan , Yu Shaobin , Huang Zhixin , Xu Hui , Kang Mingqiang
Published: May 2022

Endoscopic resection is increasingly used to treat patients with pathological T1 (pT1) esophageal squamous cell carcinoma (ESCC) because of its small surgical trauma. However, reports of the risk factors for lymph node metastasis (LNM) have been controversial. Therefore, we aim to build a nomogram to individually predict the risk of LNM in pT1 ESCC patients, to make an optimal balance between surgical trauma and surgical income.

One hundred seventy patients with pT1 esophageal cancer in our hospital were analyzed retrospectively. Logistic proportional hazards models were conducted to find out the risk factor associated with LNM independently, and those were imported into R library “RMS” for analysis. A nomogram is generated based on the contribution weights of variables. Finally, decision analysis and clinical impact curve were used to determine the optimal decision point.

Twenty-five (14.7%) of the 170 patients with pT1 ESCC exhibited LNM. Multivariable logistic regression analysis showed that smoking, carcinoembryonic antigen, vascular tumor thromboembolus, and tumor differentiation degree were independent risk factors for LNM. The nomogram had relatively high accuracy (C index of 0.869, 95% confidence interval: 0.794–0.914, P < .0001). The decision curve analysis provided the most significant clinical benefit for the entire included population, with scores falling just above the total score of 85 in the nomogram.

Smoking, carcinoembryonic antigen, vascular tumor thromboembolus, and tumor differentiation degree may predict the risk of LNM in tumor 1 ESCC. The risk of LNM can be predicted by the nomogram.
STROBE: The relationship between asthma and early menarche in Korean adolescents
Authors: Han Chang Hoon , Chung Jae ho , Kim Soo Rim
Published: May 2022

We explored the relationship between asthma and early menarche in a representative sample of Korean adolescents.

Web-based self-reported data collected from 2006 to 2015 by the Korean Youth Risk Behavior Web-based Survey were used. Menarche status was divided into “early” (<12 years of age, n = 69,520) and “not early” (≥12 years of age, n = 234,065).

Adolescent girls with early menarche exhibited a higher incidence of asthma (8.1% vs 7.4%, P < .001), more frequent school absences because of asthma (10.8% vs 8.7%), and more frequent ≤4-day stretches of school absence (4.6% vs 2.4%) compared with girls with “not early” menarche (all P < .001). Multivariate analysis performed after adjusting for multiple confounders revealed a 1.04-fold (95% confidence interval [CI] 1.00–1.07) greater likelihood of asthma in the early menarche than not early menarche group. In addition, the odds ratios for missing school due to asthma for 1 to 3 and ≥4 days per year in the early menarche group were 1.00 (95% CI 1.00–1.02) and 1.21 (95% CI 1.01–1.46), respectively.

Adolescents with early menarche exhibited increased incidences of asthma and severe asthma.
Thrombotic thrombocytopenic purpura (TTP) in Human immunodeficiency virus (HIV) infected patients: New twists on an old disease
Authors: Louw Susan , Gededzha Maemu P. , Mayne Anthony L. , Mayne Elizabeth S.
Published: May 2022

Objective:

Investigate the presence of inflammation, endothelial dysfunction and complement activation in patients with HIV-associated thrombotic thrombocytopenic purpura (HIV-TTP) to support the hypothesis that these processes probably contribute to the development of this thrombotic microangiopathy.

Design:

A prospective, investigational cohort study of 35 consecutive patients diagnosed with HIV-associated TTP presenting to three academic, tertiary care hospitals in Johannesburg, South Africa over 2 years.

Methods:

The patients with HIV-TTP received therapeutic plasma therapy and supportive treatment. Demographic data, the results of routine investigations and patient outcomes were recorded. Peripheral blood samples were collected prior to and on completion of plasma therapy and the following additional parameters were assessed at both time points: activity of the von Willebrand factor (VWF) cleaving protease, a-disintegrin-and-metalloproteinase-with-thrombospondin-motifs 13 (ADAMTS-13) and the presence of ADAMTS-13 autoantibodies, levels of pro-inflammatory cytokines, interleukin-6 and tumour necrosis factor-alpha, and two endothelial cell adhesion molecules. Complement activation was assessed by sequential measurement of C3 and C4 as well as levels of the complement inhibitor, factor H.

Results:

The inflammatory and endothelial activation markers were significantly (P < 0.001) elevated in the cohort of patients prior to plasma therapy compared with levels on discharge. Complement was activated and normalized with therapy. The ADAMTS-13 levels were reduced with significant auto-antibodies to this protease at presentation.

Conclusion:

Inflammation in HIV mediates endothelial damage and complement activation. This study proposes that these processes are probably contributory to the development of HIV-TTP, which can therefore be characterized in part as a complementopathy, resembling TTP-like syndrome.
Sex differences in cytokine profiles during suppressive antiretroviral therapy
Authors: Vanpouille Christophe , Wells Alan , Wilkin Timothy , Mathad Jyoti S. , Morris Sheldon , Margolis Leonid , Gianella Sara
Published: May 2022

Objective:

Despite lower plasma HIV RNA levels, women progress faster to AIDS than men. The reasons for these differences are not clear but might be a consequence of an elevated inflammatory response in women.

Methods:

We investigated sex differences in cytokine profiles by measuring the concentrations of 36 cytokine/chemokines by Luminex in blood of women and men (sex at birth) with chronic HIV infection under suppressive therapy. We initially performed a principal component analysis to see if participants clustered by sex, and then fit a partial least squares discriminant analysis (PLS-DA) model where we used cytokines to predict sex at birth. The significance of the difference in nine cytokines with VIP greater than 1 was tested using Wilcoxon test-rank. Further, potential confounding factors were tested by multivariate linear regression models.

Results:

Overall, we predicted sex at birth in the PLS-DA model with an error rate of approximately 13%. We identified five cytokines, which were significantly higher in women compared with men, namely the pro-inflammatory chemokines CXCL1 (Gro-α), CCL5 (RANTES), CCL3 (MIP-1α), CCL4 (MIP-1β), as well as the T-cell homeostatic factor IL-7. The effect of sex remained significant after adjusting for CD4+, age, ethnicity, and race for all cytokines, except for CCL3 and race.

Conclusion:

The observed sex-based differences in cytokines might contribute to higher immune activation in women compared with men despite suppressive therapy. Increased levels of IL-7 in women suggest that homeostatic proliferation may have a differential contribution to HIV reservoir maintenance in female and male individuals. Our study emphasizes the importance of sex-specific studies of viral pathogenesis.
Falls from ladders: Injury patterns and outcomes
Authors: Liasidis Panagiotis K. , Jakob Dominik A. , Schellenberg Morgan , Matsushima Kazuhide , Lam Lydia , Lewis Meghan R. , Demetriades Demetrios , Inaba Kenji
Published: May 2022

BACKGROUND

Our contemporary understanding of the impact of falls from ladders remains limited. The purpose of this study was to examine the injury patterns and outcomes of falls from ladders. Our hypothesis was that age affects both injury type and outcomes.

METHODS

The National Trauma Data Bank was queried for all patients who fell from a ladder (January 2007 to December 2017). Participants were stratified into four groups according to age: 15 years or younger, 16 years to 50 years, 51 years to 65 years, and older than 65 years. Univariate and multivariate analyses were performed to compare the injury patterns and outcomes between the groups.

RESULTS

A total of 168,227 patients were included for analysis. Median age was 56 years (interquartile range, 45–66 years), 86.1% were male, and median ISS was 9 (interquartile range, 4–13). Increasing age was associated with a higher risk of severe trauma (ISS > 15: 8.8% vs. 13.7% vs. 17.5% vs. 22.0%; p < 0.001). Head injuries followed a U-shaped distribution, with pediatric and elderly patients representing the most vulnerable groups. Overall, fractures were the most common type of injury, in the following order: lower extremity, 27.3%; spine, 24.9%; rib, 23.1%; upper extremity, 20.1%; and pelvis, 10.3%. The overall intensive care unit admission rate was 21.5%; however, it was significantly higher in the elderly (29.1%). In-hospital mortality was 1.8%. The risk of death progressively increased with age with a mortality rate of 0.3%, 0.9%, 1.5%, and 3.6%, respectively (p < 0.001). Strong predictors of mortality were Glasgow Coma Scale score of 8 or lower on admission (odds ratio, 29.80; 95% confidence interval, 26.66–33.31; p < 0.001) and age >65 years (odds ratio 4.07; 95% confidence interval, 3.535–4.692; p < 0.001). Only 50.8% of the elderly patients were discharged home without health services, 16.5% were discharged to nursing homes, and 15.2% to rehabilitation centers.

CONCLUSION

Falls from ladders are associated with considerable morbidity and mortality, especially in the elderly. Head injuries and fractures are common and often severe. An intensified approach to safe ladder use in the community is warranted.

LEVEL OF EVIDENCE

Therapeutic/care management; Level III.
Individual differences in adapting to temperature in French students are only related to attachment avoidance and loneliness
Authors: Wittmann Adrien , Braud Mae , Dujols Olivier , Forscher Patrick , IJzerman Hans
Published: May 2022

Among animals, natural selection has resulted in a broad array of behavioural strategies to maintain core body temperature in a relatively narrow range. One important temperature regulation strategy is
social thermoregulation
, which is often done by warming the body together with conspecifics. The literature suggests that the same selection pressures that apply to other animals also apply to humans, producing individual differences in the tendency to socially thermoregulate. We wanted to investigate whether differences in social thermoregulation desires extend to other personality factors in a sample of French students. We conducted an exploratory, hypothesis-generating
cross-sectional
project to examine associations between thermoregulation and personality. We used conditional random forests in a training segment of our dataset to identify clusters of variables most likely to be shaped by individual differences to thermoregulate. We used the resulting clusters to fit hypothesis-generating mediation models. After we replicated the relationships in two datasets, personality was not related to social thermoregulation desires, with the exception of attachment avoidance. Attachment avoidance in turn predicted loneliness. This mediation proved robust across all three datasets. As our cross-sectional studies allow limited causal inferences, we suggest investing into prospective studies to understand whether and how social thermoregulation shapes attachment avoidance early in life and loneliness later in life. We also recommend replication of the current relationships in other climates, countries, and age groups.
Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera)
Authors: Li Ting Ting , Zhang Hong Xia , Gu Chun Tao
Published: May 2022

A novel bifidobacteria (designated S053-2T) was isolated from the gut of honeybee (Apis mellifera). Strain S053-2T was characterized using a polyphasic taxonomic approach. The result of 16S rRNA gene sequence analysis indicated that strain S053-2T was phylogenetically related to the type strains of

Bifidobacterium asteroides

,

Bifidobacterium indicum

,

Bifidobacterium actinocoloniiforme

,

Bifidobacterium xylocopae

,

Bifidobacterium coryneforme

,

Bifidobacterium apousia

,

Bifidobacterium choladohabitans

and

Bifidobacterium polysaccharolyticum

, and had 95.5–99.7 % 16S rRNA gene sequence similarities. Based on the 16S rRNA gene sequence analysis, strain S053-2T was most closely related to the type strain of

B. asteroides

, having 99.7 % 16S rRNA gene sequence similarity. Strain S053-2T had relatively low (91.6–95.7 %) pheS, atpA, clpC, dnaG, fusA, glnA, glyS, hsp60, argS, pyrG and recA sequence similarities to the type strain of

B. asteroides

. Strain S053-2T had 94.5–95.3% atpA, clpC, dnaG, dnaK and pyrG sequence similarities to the type strain of

B. apousia

. The phylogenomic tree indicated that strain S053-2T belonged to the

B. asteroides

group, and was most closely related to the type strains of

B. asteroides

,

B. apousia

,

B. choladohabitans

and

B. polysaccharolyticum

, and distantly related to type strains of other phylogenetically related species in the

B. asteroides

group. Strain S053-2T shared the highest average nucleotide identity (ANI, 93.8 %), digital DNA–DNA hybridization (dDDH, 52.4 %) and average amino acid identity (AAI, 95.6%) values with

B. apousia

W8102T. Strain S053-2T shared 91.1 % ANI, 41.9 % dDDH and 92.5 % AAI values with

B. asteroides

DSM 20089T. Acid production from l-arabinose, d-xylose, d-mannose, amygdalin, cellobiose, maltose, melibiose, sucrose, raffinose, gentiobiose and l-fucose, and activity of esterase lipase (C8) and α-fucosidase could differentiate strain S053-2T from

B. asteroides

DSM 20089T. Acid production from d-mannose, maltose, sucrose, melezitose and gentiobiose, and activity of α-fucosidase could differentiate strain S053-2T from

B. apousia

W8102T. Based upon the data obtained in the present study, a novel species, Bifidobacterium mizhiense sp. nov., is proposed, and the type strain is S053-2T (=JCM 34710T=CCTCC AB 2021129T).
Physical resilience in the brain: The effect of white matter disease on brain networks in cognitively normal older adults
Authors: Neyland Blake R , Lockhart Samuel N , Lyday Robert G , Baker Laura D , Handing Elizabeth P , Miller Michael E , Kritchevsky Stephen B , Laurienti Paul J , Hugenschmidt Christina E
Published: May 2022

BACKGROUND

Physical resilience with age is considered a key feature of healthy aging, but current understanding of the neural contributions to resilience is limited. Additionally, few methods exist to identify physical resilience and observe the mechanisms through which resilience manifests.

METHODS

To address these gaps, we used data from 189 participants from the Brain Networks and Mobility (B-NET) study who completed the short physical performance battery (SPPB) as well as its expanded version (eSPPB), magnetic resonance imaging (MRI), and functional MRI (fMRI). Functional brain networks were generated using graph theory methods. We grouped participants based on SPPB scores (<10=unhealthy & 10-12=healthy) and median splits of white matter hyperintensity volumes: Expected Healthy (EH: low WMH, healthy SPPB, n=81), Expected Impaired (EI: high WMH, unhealthy SPPB, n=42), Unexpected Healthy (UH: high WMH, healthy SPPB, n=53), and Unexpected Impaired (UI: low WMH, unhealthy SPPB, n=13). UH is considered the “resilient” group due to their maintained function despite elevated WMH burden. Continuous analyses assessed the relationships between network properties, mobility, and cognition.

RESULTS

Higher SPPB scores were associated (p<0.01) with greater sensorimotor cortex community structure (SMN-CS) consistency. While no main effect of the resilience interaction term (SPPB*WMH) was found on SMN-CS, UH showed higher numbers of second-order connections between the SMN and anterior cingulate cortex (ACC) than EI (p<0.01).

CONCLUSIONS

Increased connectivity between SMN and ACC may be a marker of physical resilience within the brain.
Topological Data Analysis of Thoracic Radiographic Images shows Improved Radiomics-based Lung Tumor Histology Prediction
Authors: Vandaele Robin , Mukherjee Pritam , Selby Heather Marie , Shah Rajesh Pravin , Gevaert Olivier
Published: May 2022

Topological data analysis (TDA) provides unparalleled tools to capture local to global structural shape information in data. In particular, its main method under the name of persistent homology has found many recent successful applications to both supervised and unsupervised machine learning. Despite its recent gain in popularity, much of its potential for medical image analysis remains undiscovered. In this paper we explore the prominent learning problems on thoracic radiographic images of lung tumors to which persistent homology provides improvements over state-of-the-art radiomic-based learning. It turns out that the novel topological features well capture complementary information important for both ‘benign vs. malignant ‘ and ‘adenocarcinoma vs. squamous cell carcinoma’ tumor prediction, while contributing less consistently to ‘small cell vs. non-small cell ‘—an interesting result in its own right. Furthermore, while radiomic features may be better at predicting malignancy scores assigned by expert radiologists based on visual inspection, it turns out that topological features may be better at predicting the more accurate tumor histology assessed through long-term radiology review, biopsy, surgical resection, progression or response.
When Online Citizen Science meets Teaching: Storyfication of a science discovery game to teach, learn, contribute to genomic research
Authors: Drogaris Chrisostomos , Butyaev Alexander , Nazarova Elena , Sarrazin-Gendron Roman , Patel Harsh , Singh Akash , Kadota Brenden , Waldispühl Jérôme
Published: May 2022

In the last decade, video games became a common vehicle for citizen science initiatives in life science, allowing participants to contribute to real scientific data analysis while learning about it. Since 2010, our scientific discovery game (SDG) Phylo enlists participants in comparative genomic data analysis. It is frequently used as a learning tool, but the activities were difficult to aggregate to build a coherent teaching activity. Here, we describe a strategy and series of recipes to facilitate the integration of SDGs in courses and implement this approach in Phylo. We developed new roles and functionalities enabling instructors to create assignments and monitor the progress of students. A story mode progressively introduces comparative genomics concepts, allowing users to learn and contribute to the analysis of real genomic sequences. Preliminary results from a user study suggest this framework may help to boost user motivation and clarify pedagogical objectives.
Revisiting Colocalization from the Perspective of Similarity
Authors: da Fontoura Costa Luciano
Published: May 2022

Given two or more concentrations, an interesting and important related issue concerns the quantification of how strongly they are spatially interrelated. The concept of colocalization has been frequently considered as an indication of the tendency of the values of two concentrations to spatially vary together. While this frequently adopted approach presents several interesting characteristics, being a suitable choice for several situations, in the present work we study how multiset similarity indices can be applied for similar purposes, possibly allowing a complementation, in the sense of taking into account shared portions of the concentrations, of the colocalization characterization provided by the Pearson correlation methodology. The problem of colocalization is first addressed in terms of possible underlying mathematical models, and then the Pearson correlation coefficient-based approach, as well as the standardization procedure which is its intrinsic part, are presented and discussed. The particularly important issue of how to define the baseline of the concentrations is also approached and illustrated. The minmax alternative normalization scheme is presented next, followed by the description of the three considered multiset simiarlity indices — namely the interiority, Jaccard, and coincidence similarity approaches. The characteristics of each of these methods is then illustrated respectively to 1D, and then to 2D concentrations under presence of several interesting and relevant effects including spatial displacement, as well as sharpening, presence of unrelated effects. The similarity indices, and in particular the coincidence approach, are found to present some interesting features when applied to the quantification of the colocalization between two or more concentrations, suggesting that it can provided complementary information when performing colocalization analysis.
Uncovering Lasonolide A biosynthesis using genome-resolved metagenomics
Authors: Uppal Siddharth , Metz Jackie L. , Xavier René K.M. , Nepal Keshav , Xu Dongbo , Wang Guojun , Kwan Jason C.
Published: May 2022

Invertebrates, in particular sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anti-cancer molecule isolated from the marine spongeForcepiasp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60 cell line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of theForcepiasponge metagenome revealed a gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed this bacterium, herein namedCandidatusThermopylae lasonolidus, only has 88.78% 16S rRNA identity with the closest relativePedosphaera parvulaEllin514, indicating it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as atrans-AT polyketide synthase (PKS) pathway. When compared with its host genome, thelasBGC exhibits a significantly different GC content and penta-nucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putativelaspathway were identified in the candidate producer genome. Differences between the threelasrepeats were observed including the presence of three insertions, two single-nucleotide polymorphisms and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the Verrucomicrobial producer shows signs of genome-reduction, its genome size is still fairly large (about 5Mbp) and when compared to its closest free-living relative contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction.

Importance

While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small amounts by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine spongeForcepiasp., is a cytotoxic molecule active at nanomolar concentrations and causes premature chromosome condensation, blebbing, cell contraction and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anti-cancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome ofForcepiasp. using culture-independent DNA sequencing to uncover how an uncultured bacterium produces LSA. This provides future opportunities for heterologous expression and cultivation efforts that may minimize LSA’s supply problem.
Multiple roles of Pax6 in corneal limbal epithelial cells and maturing epithelial cell adhesion
Authors: Sunny Sweetu Susan , Lachova Jitka , Dupacova Naoko , Kozmik Zbynek
Published: May 2022

Mammalian corneal development is a multistep process, including formation of corneal epithelium (CE), endothelium and stroma during embryogenesis followed by postnatal stratification of the epithelial layers, and continuous renewal of the epithelium to replace the most outer corneal cells. Herein we employed Cre-loxPsystem to conditionally deplete Pax6 proteins in two domains of ocular cells, including the ocular surface epithelium (cornea, limbus and conjunctiva) or postnatal CE, viaK14-creorAldh3-cre, respectively. Earlier and broader inactivation of Pax6 in the OSE resulted in thickened OSE with CE and limbal cells adopting the conjunctival keratin expression pattern. More restricted depletion of Pax6 in postnatal CE resulted in the abnormal cornea marked by reduced epithelial thickness despite of increased epithelial cell proliferation. Immunofluorescence studies showed loss of Keratin 12, an intermediate filament and diffused expression of adherens junction components, together with reduced tight junction protein, Zonula occludens-1 (ZO-1). Furthermore, expression of Keratin 14, basal cell marker in apical layers, indicates impaired differentiation of corneal epithelial cells. Collectively, our data demonstrate that Pax6 is essential for maintaining proper differentiation and strong intercellular adhesion in postnatal corneal epithelial cells, whereas limbal Pax6 is required for preventing the outgrowth of conjunctival cells to the cornea.
Lossless indexing with counting de Bruijn graphs
Authors: Karasikov Mikhail , Mustafa Harun , Rätsch Gunnar , Kahles André
Published: May 2022

Sequencing data are rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated (or colored) de Bruijn graphs for efficiently indexing k-mer sets. However, approaches for representing quantitative attributes such as gene expression or genome positions in a general manner have remained underexplored. In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by supplementing each node–label relation with one or many attributes (e.g., a k-mer count or its positions). Counting de Bruijn graphs index k-mer abundances from 2652 human RNA-seq samples in over eightfold smaller representations compared with state-of-the-art bioinformatics tools and is faster to construct and query. Furthermore, counting de Bruijn graphs with positional annotations losslessly represent entire reads in indexes on average 27% smaller than the input compressed with gzip for human Illumina RNA-seq and 57% smaller for Pacific Biosciences (PacBio) HiFi sequencing of viral samples. A complete searchable index of all viral PacBio SMRT reads from NCBI's Sequence Read Archive (SRA) (152,884 samples, 875 Gbp) comprises only 178 GB. Finally, on the full RefSeq collection, we generate a lossless and fully queryable index that is 4.6-fold smaller than the MegaBLAST index. The techniques proposed in this work naturally complement existing methods and tools using de Bruijn graphs, and significantly broaden their applicability: from indexing k-mer counts and genome positions to implementing novel sequence alignment algorithms on top of highly compressed graph-based sequence indexes.
Crystal structure and Hirshfeld surface analysis of methyl 4′-amino-3′,5′-dicyano-2,2′′-dioxodispiro[indoline-3,1′-cyclopentane-2′,3′′-indolin]-3′-ene-5′-carboximidate with an unknown solvent
Authors: Naghiyev Farid N. , Khrustalev Victor N. , Fortalnova Elena A. , Akkurt Mehmet , Khalilov Ali N. , Bhattarai Ajaya , Mamedov İbrahim G.
Published: May 2022

In the title compound, C23H16N6O3, the central five-membered cyclopentene ring adopts an envelope conformation while the five-membered spiro 2,3-dihydro-1H-pyrrole rings exhibit twisted envelope and envelope conformations. One of the 1,3-dihydro-2H-indol-2-one units is in an axial position and the other is in a bisectional position. The methyl methanimidate unit is in an equatorial position. The crystal structure of the title compound is consolidated by intermolecular N—H...N, N—H...O and C—H...O hydrogen bonds, forming a three dimensional network.
Financial and economic risk management in coastal land reclamation projects
Authors: Perera Hashan Pubudu , Perera B.A.K.S. , Palihakkara Asha Dulanjalie
Published: May 2022

Purpose

Coastal land reclamation (CLR) projects have become an effective solution for population growth while creating new market areas and expanding revenue streams. Although a few studies have been conducted on risk management in CLR projects, they had very little prioritisation on financial and economic risk management. Thus, this study aims to manage the financial and economic risks of CLR projects.

Design/methodology/approach

A quantitative research approach consisting of three Delphi rounds was adopted for this study. The findings of this study were analysed and validated using statistical tools.

Findings

This study identified 13 significant financial and economic risk factors in CLR projects, among which poor quality of the sand and soil, delays in making payments, unpredictability of the safety and security of the country and high dredging volumes were the most significant. Most of these risks have to be borne by the client and the contractor. Conducting environmental impact studies, following quality control procedures and increasing social awareness are significant strategies to handle the financial and economic risks of CLR projects.

Originality/value

This study addresses the literature gap pertaining to financial and economic risk management in CLR projects by identifying its overall process, including the identification of significant financial and economic risks based on the severity levels; risk allocation among the client, contractor and consultant; and suitable risk handling strategies for each significant financial and economic risk factor. Moreover, the findings of this study can be used to effectively deal with financial and economic risks in CLR projects while raising society’s awareness.
Slicing vs chunking product-harm crisis: antecedents and firm performance implications
Authors: Pupovac Ljubomir , Carrillat François Anthony , Michayluk David
Published: May 2022

Purpose

The high prevalence of product-harm crises (PHC) represents a continuing challenge to which firms sometimes react by announcing several smaller recalls (i.e. slicing) but at other times by announcing the recall of all faulty products at once (i.e. chunking). The slicing vs chunking phenomenon has not been identified by prior literature; this study aims to explore two research questions: Why do firms sometimes slice and other times chunk PHC? Do slicing and chunking affect firm performance differently?

Design/methodology/approach

The authors examined recall guidelines from the US National Highway Traffic Safety Administration (NHTSA) and conducted expert interviews as well as a quantitative analysis of 378 product recalls to determine the antecedents of slicing vs chunking. The authors further performed an event study to examine the impact of slicing vs chunking PHCs on firms’ financial performance.

Findings

The authors find that slicing vs chunking is not a deliberate strategy but rather the consequence of firms’ resource availability and constraints. Furthermore, the authors show that larger firms have a lower likelihood of slicing versus chunking. By contrast, larger R&D expenditures, and greater reputation, as well as larger recall sizes, increase the likelihood of slicing versus chunking. Finally, the results reveal that, compared to chunking, slicing PHC has a strong negative impact on firms’ stock value.

Research limitations/implications

The authors relied on recalls in the US automobile industry. A possible extension would be to study the same phenomenon in other industries or other geographical areas. In addition, the results need to be generalized to other types of negative news that can be either decoupled (slicing) or coupled (chunking), especially negative news for which firms have more discretion regarding the timing of their announcements than for product recalls.

Practical implications

As shown by prior research (Eilert et al., 2017), firms should aim to announce recalls quickly in the wake of a PHC. Importantly though, the results indicate that speed should not come at the expense of comprehensiveness in identifying all defective products, so that only one recall is needed. As suggested by our findings about PHC, investors may react negatively to the slicing of other types of negative news; thus, the results suggest how to best communicate to external stakeholders during crises in general.

Originality/value

To the best of the authors’ knowledge, this is the first study that examines why firms sometimes slice and at other times chunk PHC and identifies the performance implications of these two types of recalls in response to PHC.