bluuebunny/crossref_metadata_2025_split huggingface dataset:
IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome
Authors: Desai Sanket , Rane Aishwarya , Joshi Asim , Dutt Amit 
Published: May 2021

Abstract
Background
Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate.

Results
We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.0, to perform genomic analysis to understand the variability and dynamics of the virus. It adopts the recent clade nomenclature and demonstrates the clade prediction accuracy of 92.8%. IPD 2.0 also contains a SARS-CoV-2 updater module, allowing automatic upgrading of the variant database using genome sequences from GISAID. As a proof of principle, analyzing 208,911 SARS-CoV-2 genome sequences, we generate an extensive database of 2.58 million sample-wise variants. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil and data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution.

Conclusions
A novel and dynamic feature of the SARS-CoV-2 module of IPD 2.0 makes it a contemporary tool to analyze the diverse and growing genomic strains of the virus and serve as a vital tool to help facilitate rapid genomic surveillance in a population to identify variants involved in breakthrough infections. IPD 2.0 is freely available from http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and the web-application is available at http://ipd.actrec.gov.in/ipdweb/.
Lactobacillus rhamnosus HDB1258 modulates gut microbiota-mediated immune response in mice with or without lipopolysaccharide-induced systemic inflammation
Authors: Han Sang-Kap , Shin Yeon-Jeong , Lee Dong-Yeon , Kim Kyung Min , Yang Seo-Jin , Kim Du Seong , Choi Ji-Whi , Lee Seunghun , Kim Dong-Hyun 
Published: May 2021

AbstractBackgroundGut microbiota closely communicate in the immune system to maintain a balanced immune homeostasis in the gastrointestinal tract of the host. Oral administration of probiotics modulates gut microbiota composition. In the present study, we isolatedLactobacillus rhamnosusHDB1258, which induced tumor necrosis factor (TNF)-α and interleukin (IL)-10 expression in macrophages, from the feces of breastfeeding infants and examined how HDB1258 could regulate the homeostatic immune response in mice with or without lipopolysaccharide (LPS)-induced systemic inflammation.ResultsOral administration of HDB1258 significantly increased splenic NK cell cytotoxicity, peritoneal macrophage phagocytosis, splenic and colonic TNF-α expression, TNF-α to IL-10 expression ratio, and fecal IgA level in control mice, while Th1 and Treg cell differentiation was not affected in the spleen. However, HDB1258 treatment significantly suppressed peritoneal macrophage phagocytosis and blood prostaglandin E2 level in mice with LPS-induced systemic inflammation. Its treatment increased LPS-suppressed ratios of Treg to Th1 cell population, Foxp3 to T-bet expression, and IL-10 to TNF-α expression. Oral administration of HDB1258 significantly decreased LPS-induced colon shortening, myeloperoxidase activity and NF-κB+/CD11c+cell population in the colon, while the ratio of IL-10 to TNF-α expression increased. Moreover, HDB1258 treatment shifted gut microbiota composition in mice with and without LPS-induced systemic inflammation: it increased the Cyanobacteria and PAC000664_g (belonging to Bacteroidetes) populations and reduced Deferribacteres and EU622763_s group (belonging to Bacteroidetes) populations. In particular, PAC001066_g and PAC001072_s populations were negatively correlated with the ratio of IL-10 to TNF-α expression in the colon, while the PAC001070_s group population was positively correlated.ConclusionsOral administered HDB1258 may enhance the immune response by activating innate immunity including to macrophage phagocytosis and NK cell cytotoxicity in the healthy host and suppress systemic inflammation in the host with inflammation by the modulation of gut microbiota and IL-10 to TNF-α expression ratio in immune cells.
Phenotypic changes in group B streptococci grown in the presence of the polyols, erythritol, sorbitol and mannitol
Authors: Hulbah Maram , Croxen Matthew A. , Tyrrell Gregory J. 
Published: May 2021

Abstract
Background
Group B streptococci (GBS) are important neonatal bacterial pathogens that can cause severe invasive disease in the newborn. It is thought that in many cases of invasive neonatal GBS disease, the bacteria ascend the vagina into the uterus and infect the amniotic fluid surrounding the fetus. Important constituents of this environment include the polyols or sugar alcohols of which erythritol, sorbitol and mannitol are examples. The aim of our study was to investigate the effect of polyols on GBS grown in media containing these sugar alcohols.

Results
GBS incubated in varying concentrations of polyols (erythritol, sorbitol or mannitol) did not display any significant enhancement or inhibition of bacterial growth. However, growth of GBS in the presence of erythritol significantly increased the surface expression of GBS-PGK (a plasminogen binding protein) 1.25 to 1.5-fold depending on the erythritol concentration and significantly enhanced the survival in human blood 3X to 18X depending on the concentration of polyol used. Interestingly, GBS grown in 1% erythritol significantly increased invasion by the bacteria of HeLa cells (epithelial cell line) (150% vs 100%) however, at higher concentrations (2% or 4% of polyol) the number of CFUs was significantly reduced (55-75% vs 100%) suggesting higher concentrations of polyols may inhibit invasion. Erythritol also increased GBS hemolytic activity as well as enhancing biofilm formation 1.4X to 3.3X depending on the concentration of polyol used.

Conclusions
GBS grown in the presence of polyols alters the bacteria’s phenotype resulting in changes associated with GBS virulence. This effect was greatest for the polyol erythritol.
A qualitative study of home health care experiences among Chinese homebound adults
Authors: Zhou Rui , Cheng Joyce , Wang Shuangshuang , Yao Nengliang 
Published: May 2021

Abstract
Background
Home health care services (HHC) are emerging in China to meet increased healthcare needs among the homebound population, but there is a lack of research examining the efficiency and effectiveness of this new care model. This study aimed to investigate care recipients’ experiences with HHC and areas for improvement in China.

Methods
This research was a qualitative study based on semi-structured interviews. Qualitative data were collected from homebound adults living in Jinan, Zhangqiu, and Shanghai, China. A sample of 17 homebound participants aged 45 or older (mean age = 76) who have received home-based health care were recruited. Conceptual content analysis and Colaizzi’s method was used to generate qualitative codes and identify themes.

Results
The evaluations of participants’ experiences with HHC yielded both positive and negative aspects. Positive experiences included: 1) the healthcare delivery method was convenient for homebound older adults; 2) health problems could be detected in a timely manner because clinicians visited regularly; 3) home care providers had better bedside manners and technical skills than did hospital-based providers; 4) medical insurance typically covered the cost of home care services. Areas that could potentially be improved included: 1) the scope of HHC services was too limited to meet all the needs of homebound older adults; 2) the visit time was too short; 3) healthcare providers’ technical skills varied greatly.

Conclusions
Findings from this study suggested that the HHC model benefited Chinese older adults—primarily homebound adults—in terms of convenience and affordability. There are opportunities to expand the scope of home health care services and improve the quality of care. Policymakers should consider providing more resources and incentives to enhance HHC in China. Educational programs may be created to train more HHC providers and improve their technical skills.
Differentiating malignant and benign necrotic lung lesions using kVp-switching dual-energy spectral computed tomography
Authors: Li Qi , Fan Xiao , Luo Tian-You , Lv Fa-Jin , Huang Xing-Tao 
Published: May 2021

Abstract
Background
Necrotic pulmonary lesions manifest as relatively low-density internally on contrast-enhanced computed tomography (CT). However, using CT to differentiate malignant and benign necrotic pulmonary lesions is challenging, as these lesions have similar peripheral enhancement. With the introduction of dual-energy spectral CT (DESCT), more quantitative parameters can be obtained and the ability to differentiate material compositions has been highly promoted. This study investigated the use of kVp-switching DESCT in differentiating malignant from benign necrotic lung lesions.

Methods
From October 2016 to February 2019, 40 patients with necrotic lung cancer (NLC) and 31 with necrotic pulmonary mass-like inflammatory lesion (NPMIL) were enrolled and underwent DESCT. The clinical characteristics of patients, CT morphological features, and DESCT quantitative parameters of lesions were compared between the two groups. Binary logistic regression analysis was performed to identify the independent prognostic factors differentiating NPMIL from NLC. Receiver operating characteristic (ROC) curves were used to assess the diagnostic performance of single-parameter and multiparametric analyses.

Results
Significant differences in age, C-reactive protein concentration, the slope of the spectral curve from 40 to 65 keV (K40–65 keV) of necrosis in non-contrast-enhanced scanning (NCS), arterial phase (AP) and venous phase (VP), effective atomic number of necrosis in NCS, and iodine concentration (IC) of the solid component in VP were observed between groups (all p < 0.05). The aforementioned parameters had area under the ROC curve (AUC) values of 0.747, 0.691, 0.841, 0.641, 0.660, 0.828, and 0.754, respectively, for distinguishing between NLC and NPMIL. Multiparametric analysis showed that age, K40–65 keV of necrosis in NCS, and IC of the solid component in VP were the most effective factors for differentiating NLC from NPMIL, with an AUC of 0.966 and percentage of correct class of 88.7%.

Conclusions
DESCT can differentiate malignant from benign necrotic lung lesions with a relatively high accuracy.
Compression therapy using surgical gloves does not prevent paclitaxel-induced peripheral neuropathy: results from a double-blind phase 2 trial
Authors: Kotani Haruru , Terada Mitsuo , Mori Makiko , Horisawa Nanae , Sugino Kayoko , Kataoka Ayumi , Adachi Yayoi , Gondou Naomi , Yoshimura Akiyo , Hattori Masaya , Sawaki Masataka , Takahata Chihoko , Kobara Makiko , Iwata Hiroji 
Published: May 2021

Abstract
Background
Chemotherapy-induced peripheral neuropathy (CIPN) is a common adverse effect of paclitaxel (PTX). There is no known prophylactic measure, although there are some reports of prevention with compression therapy using surgical gloves. On account of its predominantly subjective symptoms, it is difficult to exclude bias when assessing for CIPN. In this study, we assessed the effectiveness of the same procedure for the prevention of paclitaxel-induced PN based on a double-blind study design.

Methods
The patients with early and recurrent breast cancer (with no prior PTX exposure) initiating weekly chemotherapy with PTX 80 mg/m2 were enrolled. Each patient donned two gloves on each hand at every PTX infusion. Two one-size-smaller gloves were donned on one hand (study side) and two normal-size gloves were donned on the other hand (control side) during 90 min from 30 min before the infusion to 30 min after the end of the infusion. Study side are blind for both patients and assessing physicians according to determination of the study side by research nurses in the chemotherapy unit.
The primary outcome was the difference in the frequency of CIPN (motor/sensory) determined by the physician using the common terminology criteria for adverse events (CTCAE v4.0), with an evaluation at each cycle of PTX infusion. McNemar test was used to assess the primary outcome.

Results
Between July 2017 and November 2018, 56 patients were enrolled and 49 patients were evaluated. Overall, Grade ≥ 2 PN (sensory) was observed in 30.6 and 36.7% in the study and control sides, respectively (McNemar p = 0.25). PN (motor) was observed in 4.1 and 6.1% in the study and control sides, respectively (McNemar p = 1.0).

Conclusion
Surgical glove compression therapy showed no statistically significant effect on the incidence of PTX-induced PN.

Trial registrations
This study was registered with the University Hospital Medical Information Network (UMIN) Clinical Trials Registry managed by the National University Hospital Council of Japan (UMIN000027944). Registered 26 June 2017.
Risk and outcome of subsequent malignancies after radioactive iodine treatment in differentiated thyroid cancer patients
Authors: Mei Xiaoran , Yao Xiaoqin , Feng Fang , Cheng Weiwei , Wang Hui 
Published: May 2021

Abstract
Background
We identified differentiated thyroid cancer (DTC) survivors from SEER registries and performed Poisson regression to calculate the relative risks (RRs) of subsequent malignancies (SMs) by different sites associated with radioactive iodine (RAI) treatment, and the attributable risk proportion of RAI for developing different SMs.

Results
We identified 4628 of 104,026 DTC patients developing a SM after two years of their DTC diagnosis, with a medium follow-up time of 113 months. The adjusted RRs of developing SM associated with RAI varied from 0.98 (0.58–1.65) for neurologic SMs to 1.37 (1.13–1.66) for hematologic SMs. The RRs of developing all cancer combined SMs generally increased with age at DTC diagnosis and decreased with the latency time. We estimated that the attributable risk proportion of RAI treatment is only 0.9% for all cancer combined SMs and 20% for hematologic SMs, which is the highest among all SMs. The tumor features and mortalities in patients treated with and without RAI are generally comparable.

Conclusion
With the large population based analyses, we concluded that a low percentage of DTC survivors would develop SMs during their follow-up. Although the adjusted RR of SMs development increased slightly in patients receiving RAI, the attributable risk proportion associated with RAI was low, suggesting the absolute number of SMs induced by RAI in DTC survivors would be low. The attributable risk proportion of RAI treatment is the highest in hematological SMs, but when in consideration of its low incidence among all DTC survivors, the absolute number of hematological SMs was low.
Elevated mature monocytes in bone marrow accompanied with a higher IPSS-R score predicts a poor prognosis in myelodysplastic syndromes
Authors: Wu An , Gao Panpan , Wu Ningning , Shi Cong , Huang Zhenya , Rong Chunmeng , Sun Ye , Sheng Lixia , Ouyang Guifang , Mu Qitian 
Published: May 2021

Abstract
Background
Myelodysplastic syndromes (MDS) is a group of heterogeneous myeloid clonal diseases originating from hematopoietic stem cells. Clinically, elevated mature monocyte in bone marrow is often observed, but its clinical value still remains unclear.

Methods
We retrospectively analyzed a cohort of 216 MDS patients to explore the prognostic value of the percentage of mature monocyte in bone marrow (PMMBM). All patients were divided into elevated PMMBM group and the normal group by 6% PMMBM as the cut-off value.

Results
Our results showed that PMMBM> 6% was associated with inferior overall survival (OS) (P = 0.026) along with higher-risk IPSS-R (P = 0.025) and higher frequency of IDH2 mutation (P = 0.007). Multivariate analyses showed that besides older age (> 60 years) for OS, gender (male) for OS, lower neutrophil count (< 0.8 ×  109/L) for OS, higher bone marrow blast percentage (> 5%) for OS and LFS, poorer karyotype for OS, elevated PMMBM was also an independent adverse prognostic factor for OS in MDS (P < 0.0001) but not for LFS (P = 0.736).

Conclusions
These findings indicate that increased PMMBM may assists Revised International Prognostic Scoring System (IPSS-R) to predict a poor outcome and provide a novel evaluation factor for MDS patients especially when their karyotype analyses fail.
Chemotherapy-induced neutropenia and treatment efficacy in advanced non-small-cell lung cancer: a pooled analysis of 6 randomized trials
Authors: Gargiulo Piera , Arenare Laura , Gridelli Cesare , Morabito Alessandro , Ciardiello Fortunato , Gebbia Vittorio , Maione Paolo , Spagnuolo Alessia , Palumbo Giuliano , Esposito Giovanna , Della Corte Carminia Maria , Morgillo Floriana , Mancuso Gianfranco , Di Liello Raimondo , Gravina Adriano , Schettino Clorinda , Di Maio Massimo , Gallo Ciro , Perrone Francesco , Piccirillo Maria Carmela 
Published: May 2021

Abstract
Background
Chemotherapy-induced neutropenia (CIN) has been demonstrated to be a prognostic factor in several cancer conditions. We previously found a significant prognostic value of CIN on overall survival (OS), in a pooled dataset of patients with advanced non-small-cell lung cancer (NSCLC) receiving first line chemotherapy from 1996 to 2001. However, the prognostic role of CIN in NSCLC is still debated.

Methods
We performed a post hoc analysis pooling data prospectively collected in six randomized phase 3 trials in NSCLC conducted from 2002 to 2016. Patients who never started chemotherapy and those for whom toxicity data were missing were excluded. Neutropenia was categorized on the basis of worst grade during chemotherapy: absent (grade 0), mild (grade 1–2), or severe (grade 3–4). The primary endpoint was OS. Multivariable Cox model was applied for statistical analyses. In the primary analysis, a minimum time (landmark) at 180 days from randomization was applied in order to minimize the time-dependent bias.

Results
Overall, 1529 patients, who received chemotherapy, were eligible; 572 of them (who received 6 cycles of treatment) represented the landmark population. Severe CIN was reported in 143 (25.0%) patients and mild CIN in 135 (23.6%). At multivariable OS analysis, CIN was significantly predictive of prognosis although its prognostic value was entirely driven by severe CIN (hazard ratio [HR] of death 0.71; 95%CI: 0.53–0.95) while it was not evident with mild CIN (HR 1.21; 95%CI: 0.92–1.58). Consistent results were observed in the out-of-landmark group (including 957 patients), where both severe and mild CIN were significantly associated with a reduced risk of death.

Conclusion
The pooled analysis of six large trials of NSCLC treatment shows that CIN occurrence is significantly associated with a longer overall survival, particularly in patients developing severe CIN, confirming our previous findings.
Compound heterozygous missense mutations in a Chinese mucopolysaccharidosis type VI patient: a case report
Authors: He Ming-Fang , Yang Ji , Dong Meng-Jie , Wang Yin-Ting , Liu Hai 
Published: May 2021

Abstract
Background
Mucopolysaccharidosis type VI (MPS VI) is a rare autosomal recessive inherited disease caused by mutations in the arylsulfatase B (ARSB) gene. MPS VI is a multisystemic disease resulting from a deficiency in arylsulfatase B causing an accumulation of glycosaminoglycans in the tissues and organs of the body.
In this report, we present the case of a 16-year-old Chinese male who presented with vision loss caused by corneal opacity. MPS VI was confirmed by genetic diagnosis.

Case presentation
A 16-year-old Chinese male presented with a one-year history of binocular vision loss. The best-corrected visual acuity was 0.25 in the right eye and 0.5 in the left eye. Although slit-lamp examination revealed corneal opacification in both eyes, the ocular examinations of his parents were normal. At the same time, the patient presented with kyphotic deformity, short stature, joint and skeletal malformation, thick lips, long fingers, and coarse facial features. Genetic assessments revealed that ARSB was the causative gene. Compound heterozygous missense mutations were found in the ARSB gene, namely c.1325G > A (p. Thr442Met) (M1) and c.1197G > C (p. Phe399Leu) (M2). Genetic diagnosis confirmed that the patient had MPS VI.

Conclusions
This paper reports a case of MPS VI confirmed by genetic diagnosis.
MPS VI is a multisystem metabolic disease, with corneal opacity as a concomitant ocular symptom. As it is difficult for ophthalmologists to definitively diagnose MPS VI, genetic testing is useful for disease confirmation.
Differences in reporting food insecurity and factors associated with differences among Latino fathers and mothers
Authors: Nagao-Sato Sayaka , Druziako Stephanie , Baltaci Aysegul , Peralta Reyes Alejandro Omar , Zhang Youjie , Hurtado Choque Ghaffar Ali , Reicks Marla 
Published: May 2021

Abstract
Background
Food security status has been assessed as a representative score for households; however, different members in the same household may perceive and report food insecurity differently. A high prevalence of food insecurity has been reported among Latino households, therefore understanding differences in reporting food insecurity by Latino father-mother dyads may improve accuracy of assessment and plans to address food insecurity. This study aimed to 1) determine demographic characteristics and/or food-related factors associated with perceptions of food security status among Latino father-mother dyads, and 2) identify factors associated with discordance in perceptions of food insecurity between dyads.

Methods
Baseline data were used from a community-based, youth obesity prevention program among Latino families (n = 106 father-mother dyads). Food security was assessed with a 2-item food insecurity screen. Logistic regression models were used to evaluate associations between reporting food security status and predictor variables for fathers, mothers, and dyad-discordant responses.

Results
Food insecurity was reported by 39% of fathers and 55% of mothers. Adjusted odds of reporting food insecurity were significantly higher for fathers perceiving their neighborhood was unsafe vs. safe (OR: 3.7, p < 0.05) and reporting lower vs. higher household income (OR: 3.2, p < 0.05). Adjusted odds of reporting food insecurity were significantly higher for mothers perceiving their neighborhood was unsafe vs. safe (OR: 4.1, p < 0.01) and reporting lower vs. higher home availability of fruit and vegetable (OR: 5.5, p < 0.01). Dyad discordance in reporting food security status occurred in 24% of the dyads. Adjusted odds of dyad discordant reports of food insecurity status were significantly higher for dyads reporting discordant responses regarding previous nutrition education (OR: 3.4, p < 0.05) and higher home fruit and vegetable accessibility (OR: 3.1, p < 0.05) compared to dyads reporting concordant responses. Among the 28 dyads who reported discordant nutrition education participation, 21 reported that fathers had never participated but mothers had participated more than once.

Conclusions
Differential factors were associated with reporting food security among Latino father-mother dyads. Nutrition education for fathers that improves awareness of home food supplies and a better understanding of how food accessibility influences maternal perceptions may improve dyad discordance in reporting household food security.