bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome assembly ofGanoderma leucocontextum(Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China
Authors: Liu Yuanchao , Huang Longhua , Hu Huiping , Cai Manjun , Liang Xiaowei , Li Xiangmin , Zhang Zhi , Xie Yizhen , Xiao Chun , Chen Shaodan , Chen Diling , Yong Tianqiao , Pan Honghui , Gao Xiong , Wu Qingping 
Published: September 2021

AbstractGanoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. Ganoderma leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with an N50 scaffold size of 3.06 Mb, 78,206 coding sequences, and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and Ganoderma lucidum. Ganoderma leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.
Ubc1 turnover contributes to the spindle assembly checkpoint in Saccharomyces cerevisiae
Authors: Arsenault Heather E , Ghizzoni Julie M , Leech Cassandra M , Diers Anne R , Gesta Stephane , Vishnudas Vivek K , Narain Niven R , Sarangarajan Rangaprasad , Benanti Jennifer A 
Published: September 2021

Abstract
The spindle assembly checkpoint protects the integrity of the genome by ensuring that chromosomes are properly attached to the mitotic spindle before they are segregated during anaphase. Activation of the spindle checkpoint results in inhibition of the Anaphase-Promoting Complex (APC), an E3 ubiquitin ligase that triggers the metaphase–anaphase transition. Here, we show that levels of Ubc1, an E2 enzyme that functions in complex with the APC, modulate the response to spindle checkpoint activation in Saccharomyces cerevisiae. Overexpression of Ubc1 increased resistance to microtubule poisons, whereas Ubc1 shut-off sensitized cells. We also found that Ubc1 levels are regulated by the spindle checkpoint. Checkpoint activation or direct APC inhibition led to a decrease in Ubc1 levels, charging, and half-life. Additionally, stabilization of Ubc1 prevented its down-regulation by the spindle checkpoint and increased resistance to checkpoint-activating drugs. These results suggest that down-regulation of Ubc1 in response to spindle checkpoint signaling is necessary for a robust cell cycle arrest.
Preventing dataset shift from breaking machine-learning biomarkers
Authors: Dockès Jérôme , Varoquaux Gaël , Poline Jean-Baptiste 
Published: September 2021

Abstract
Machine learning brings the hope of finding new biomarkers extracted from cohorts with rich biomedical measurements. A good biomarker is one that gives reliable detection of the corresponding condition. However, biomarkers are often extracted from a cohort that differs from the target population. Such a mismatch, known as a dataset shift, can undermine the application of the biomarker to new individuals. Dataset shifts are frequent in biomedical research, e.g.,  because of recruitment biases. When a dataset shift occurs, standard machine-learning techniques do not suffice to extract and validate biomarkers. This article provides an overview of when and how dataset shifts break machine-learning–extracted biomarkers, as well as detection and correction strategies.
Disparities in Pediatric Patient Portal Activation and Feature Use
Authors: LeLaurin Jennifer H , Nguyen Oliver T , Thompson Lindsay A , Hall Jaclyn , Bian Jiang , Cho Hee Deok , Acharya Ratna , Harle Christopher A , Salloum Ramzi G 
Published: September 2021

Abstract

Objective
Disparities in adult patient portal adoption are well-documented; however, less is known about disparities in portal adoption in pediatrics. This study examines the prevalence and factors associated with patient portal activation and the use of specific portal features in general pediatrics.

Materials and methods
We analyzed electronic health record data from 2012 to 2020 in a large academic medical center that offers both parent and adolescent portals. We summarized portal activation and use of select portal features (messaging, records access and management, appointment management, visit/admissions summaries, and interactive feature use). We used logistic regression to model factors associated with patient portal activation among all patients along with feature use and frequent feature use among ever users (ie, ≥1 portal use).

Results
Among 52 713 unique patients, 39% had activated the patient portal, including 36% of patients aged 0–11, 41% of patients aged 12–17, and 62% of patients aged 18–21 years. Among activated accounts, ever use of specific features ranged from 28% for visit/admission summaries to 92% for records access and management. Adjusted analyses showed patients with activated accounts were more likely to be adolescents or young adults, white, female, privately insured, and less socioeconomically vulnerable. Individual feature use among ever users generally followed the same pattern.

Conclusions
Our findings demonstrate that important disparities persist in portal adoption in pediatric populations, highlighting the need for strategies to promote equitable access to patient portals.
The Newest Battlefield Opioid, Sublingual Sufentanil: A Proposal to Refine Opioid Usage in the U.S. Military
Authors: Kim Sharon Y , Buckenmaier Chester C , Howe Edmund G , Choi Kwang H 
Published: September 2021

ABSTRACT
There is an ongoing opioid epidemic in the USA, and the U.S. military is not immune to the health threat. To combat the epidemic, the Department of Defense (DoD) and Department of Veterans’ Affairs (DVA) issued new clinical practice guidelines and launched the Opioid Safety Initiative aimed at reducing opioid prescriptions. Furthermore, the DoD continually refined opioid protocols for acute pain on the battlefield, evolving from intramuscular morphine to intravenous morphine administration to oral transmucosal fentanyl citrate lollipops (Actiq) to finally sublingual sufentanil tablets (SSTs, Dsuvia). Interestingly, the newest introduction of SSTs into the military sparked great controversy, as there are concerns over the drug’s potential for misuse. However, although the opioid crisis may understandably foster an aversion to new candidate opioids, the therapeutic benefits of effective opioids in acute trauma settings should not be overlooked. SSTs may offer an improved analgesic option to meet the battlefield’s unmet needs with its non-invasive, sublingual delivery system and favorable pharmacologic properties that mitigate the risk for side effects, addiction, and adverse outcomes. Accordingly, this commentary aims to (1) review the evolution of opioid use on the battlefield and discuss the medical benefits and limitations of SSTs in acute trauma settings, (2) highlight the importance of chronic pain management post-deployment through evidence-based non-opioid modalities, and (3) explore avenues of future research. Ultimately, we propose that SSTs are an important improvement from existing battlefield opioids and that refining, not abandoning, opioid usage will be key to effectively managing pain in the military.
Quantization of blackjack: Quantum basic strategy and advantage
Authors: Mura Yushi , Wada Hiroki 
Published: September 2021

Abstract
Quantum computers that process information by harnessing the remarkable power of quantum mechanics are increasingly being put to practical use. In the future, their impact will be felt in numerous fields, including in online casino games. This is one of the reasons why quantum gambling theory has garnered considerable attention. Studies have shown that quantum gambling theory often yields nontrivial consequences that classical theory cannot interpret. We have formulated blackjack, one of the most famous card games, as a quantum game and found possible quantum entanglement between strategies. We also devised a quantum circuit reproducing classical blackjack. This circuit can be realized in the near future when quantum computers are commonplace. Furthermore, we showed that the player’s expectation increases compared to the classical game using quantum basic strategy, which is a quantum version of the popular basic strategy of blackjack.
Associations between coping strategies and insomnia: a longitudinal study of Japanese workers
Authors: Otsuka Yuichiro , Itani Osamu , Matsumoto Yuuki , Kaneita Yoshitaka 
Published: September 2021

Abstract

Study Objectives
Coping with stress is important because stress disturbs sleep. However, only a few longitudinal studies have investigated the association between coping and insomnia. We examined whether individuals with insomnia symptoms used more maladaptive coping strategies than individuals without insomnia symptoms, and evaluated the association between insomnia symptoms and coping strategies.

Methods
In this prospective cohort study, Japanese workers were enrolled and observed over a 2-year period. During both years, self-administered questionnaires on coping and insomnia symptoms were administered. Coping was assessed using the Brief-Coping Orientation to Problems Experienced, and insomnia symptoms were examined using the Athens Insomnia Scale. Generalized estimating equation modeling identified the effects of coping strategies on insomnia severity.

Results
In total, 1358 of 1855 workers at baseline were followed up. Individuals with insomnia symptoms showed a higher use of maladaptive coping strategies and less use of humor and instrumental support than individuals without insomnia symptoms. Active coping, humor, emotional support, and instrumental support were negatively associated with insomnia severity. In contrast, venting, substance use, behavioral disengagement, and self-blame were positively associated with insomnia severity.

Conclusions
This study showed that individuals with insomnia symptoms use both adaptive and maladaptive coping strategies and are more likely to use maladaptive strategies than individuals without insomnia symptoms. In the future, interventions focused on educating people about adaptive coping strategies should be conducted to determine whether coping strategies may prevent insomnia symptoms.
A case report of esophageal metastasis from breast cancer
Authors: Xu Huijun , Yang Yang , Wu Shusheng , Ke Lihong , Yan Ying , Niu Jiayu , Luo Huiqing , Chen Wenju , Li Huimin , Hu Xiaoxiu , Cao Lulu , Li Mengge , He Yifu 
Published: September 2021

Abstract

Introduction:
The common metastatic sites of breast carcinoma are the lymph nodes, liver, lungs and bone. Breast cancer metastasis to esophagus is a rarity with an incidence of 0.03% to 0.6%.

Patient concerns:
A 63-year-old woman presented with worsening dysphagia of 13 months duration. Thirteen years before, the patient had a right modified radical mastectomy and radiotherapy treatment for breast carcinoma.

Diagnosis:
Barium swallow presented a stricture of 4 cm length in the midthoracic esophagus. On endoscopy, a stricture was found in the esophageal lumen at the 28th centimeter. Biopsy showed metastatic esophageal carcinoma.

Interventions and outcomes:
Chemotherapy with gemcitabine and capecitabine was provided as the treatment. After treatment, her dysphagia markedly improved.

Conclusion:
Esophageal involvement in metastatic breast cancer is rare. Dysphagia after breast cancer treatment can indicate metastasis. Histopathologic examination is required to confirm the diagnosis.
A new smoking cessation ‘cascade’ among women with or at risk for HIV infection
Authors: Breger Tiffany L. , Westreich Daniel , Edmonds Andrew , Edwards Jessie K. , Zalla Lauren C. , Cole Stephen R. , Ramirez Catalina , Ofotokun Igho , Kassaye Seble G. , Brown Todd T. , Konkle-Parker Deborah , Jones Deborah L. , D'Souza Gypsyamber , Cohen Mardge H. , Tien Phyllis C. , Taylor Tonya N. , Anastos Kathryn , Adimora Adaora A. 
Published: September 2021

Objectives:
The aim of this study was to define a smoking cessation ‘cascade’ among USA women with and without HIV and examine differences by sociodemographic characteristics.

Design:
An observational cohort study using data from smokers participating in the Women's Interagency HIV Study between 2014 and 2019.

Methods:
We followed 1165 women smokers with and without HIV from their first study visit in 2014 or 2015 until an attempt to quit smoking within approximately 3 years of follow-up, initial cessation (i.e. no restarting smoking within approximately 6 months of a quit attempt), and sustained cessation (i.e. no restarting smoking within approximately 12 months of a quit attempt). Using the Aalen-Johansen estimator, we estimated the cumulative probability of achieving each step, accounting for the competing risk of death.

Results:
Forty-five percent of smokers attempted to quit, 27% achieved initial cessation, and 14% achieved sustained cessation with no differences by HIV status. Women with some post-high school education were more likely to achieve each step than those with less education. Outcomes did not differ by race. Thirty-six percent [95% confidence interval (95% CI): 31–42] of uninsured women attempted to quit compared with 47% (95% CI: 44–50) with Medicaid and 49% (95% CI: 41–59) with private insurance.

Conclusion:
To decrease smoking among USA women with and without HIV, targeted, multistage interventions, and increased insurance coverage are needed to address shortfalls along this cascade.
Persistence of robust humoral immune response in COVID-19 convalescent individuals over 12 months after infection
Authors: Miyakawa Kei , Kubo Sousuke , Jeremiah Sundararaj Stanleyraj , Go Hirofumi , Yamaoka Yutaro , Ohtake Norihisa , Kato Hideaki , Ikeda Satoshi , Mihara Takahiro , Matsuba Ikuro , Sanno Naoko , Miyakawa Masaaki , Shinkai Masaharu , Miyazaki Tomoyuki , Ogura Takashi , Ito Shuichi , Kaneko Takeshi , Yamamoto Kouji , Goto Atsushi , Ryo Akihide 
Published: September 2021

AbstractSARS-CoV-2 infection elicits varying degrees of protective immunity conferred by neutralizing antibodies (nAbs). Here we report the persistence of nAb responses over 12 months after infection despite its decreasing trend noticed from 6 months. The study included sera from 358 individuals who had been infected with SARS-CoV-2 between January and May 2020. Samples were collected at 6 and 12 months after onset. The titers of IgG to the viral nucleocapsid protein (NP) and receptor-binding domain of the spike protein (RBD) were measured by CLEIA. The nAb titer was determined using lentivirus-based pseudovirus or authentic virus. Antibody titers of NP-IgG, RBD-IgG, and nAbs were higher in severe and moderate cases than in mild cases at 12 months after onset. While the nAb levels were likely to confer adequate protection against wild-type viral infection, the neutralization activity to recently circulating variants in some of the mild cases (∼30%) was undermined, implying the susceptibility of reinfection to the variants of concerns (VOCs). COVID-19 convalescent individuals have robust humoral immunity even at 12 months after infection albeit that the medical history and background of patients could affect the function and dynamics of antibody response to the VOCs.
Altered prefrontal signaling during inhibitory control in a salient drug context in human cocaine addiction
Authors: Ceceli Ahmet O. , Parvaz Muhammad A. , King Sarah , Schafer Matthew , Malaker Pias , Sharma Akarsh , Alia-Klein Nelly , Goldstein Rita Z. 
Published: September 2021

AbstractDrug addiction is characterized by impaired Response Inhibition and Salience Attribution (iRISA), where the salience of drug cues is postulated to overpower that of other reinforcers with a concomitant decrease in self-control. However, the neural underpinnings of the interaction between the salience of drug cues and inhibitory control in drug addiction remain unclear. We developed a novel stop-signal fMRI task where the stop-signal reaction time (SSRT—a classical inhibitory control measure) was tested under different salience conditions (modulated by drug, food, threat or neutral words) in individuals with cocaine use disorder (CUD; n=26) vs. demographically matched healthy control participants (HC; n=26). Despite similarities in drug cue-related SSRT and valence and arousal word ratings between groups, dorsolateral prefrontal cortex (dlPFC) activity was diminished during the successful inhibition of drug versus food cues in CUD, and was correlated with lower frequency of recent use, lower craving, and longer abstinence (Z>3.1, p<.05 corrected). Results suggest altered involvement of cognitive control regions (e.g., dlPFC) during inhibitory control under a drug context, relative to an alternative reinforcer, in CUD. Supporting the iRISA model, these results elucidate the direct impact of drug-related cue-reactivity on the neural signature of inhibitory control in drug addiction.
Availability and readiness of healthcare facilities and their effects on long-acting modern contraception use in Bangladesh: Analysis of linked data
Authors: Khan Md Nuruzzaman , Islam M Mofizul , Akter Shahinoor 
Published: September 2021

AimEvidence on the availability and accessibility of health facilities and their impacts on long-acting modern contraceptives (LAMC) use in low- and middle-Income countries are scarce. This study examined the influence of the availability and readiness of health facilities in determining the use of LAMC in Bangladesh.MethodsWe linked data of the Bangladesh Demographic and Health Survey and the Health Facility Survey using the administrative-boundary linkage method. Mixed effect multilevel logistic regression was conducted. The sample comprised 10,938 married women of 15-49 years of age, who were fertile but did not desire a child within two years of the date of survey. The outcome variable was the current use of LAMC (yes, no) and the explanatory variables were health facility-, individual-, household- and community-level factors.ResultsNearly 34% of participants used LAMC with significant variations across areas in Bangladesh. The average distance between the nearest LAMC-providing health facilities and women’s homes was 6.36 km, higher in the Sylhet division (8.34 km) and lower in the Dhaka division (4.34 km). Increased scores for the management (adjusted odds ratio (AOR) 1.59; 95% CI, 1.21-2.42) and infrastructure (AOR, 1.44; 95% CI, 1.01-1.69) of health facilities were positively associated with the overall uptake of LAMC. AORs for women to report using LMAC were 2.16 (95% CI, 1.18-3.21) and 1.74 (95% CI, 1.15-3.20), respectively, for per unit increase in the availability and readiness scores to provide LAMC at the nearest health facilities. Nearly 27% decline in the likelihood of LAMC uptake was observed for every kilometer increase in the average regional-level distance between women’s homes and the nearest health facilities.ConclusionThe availability of health facilities close to residence and their improved management, infrastructure, and readiness to provide LAMC play a significant role in increasing LAMC uptake among women. Policies and programs should prioritize increasing the availability and accessibility of health facilities that provide LAMC services.
Impact of long-COVID on health-related quality of life in Japanese COVID-19 patients
Authors: Tsuzuki Shinya , Miyazato Yusuke , Terada Mari , Morioka Shinichiro , Ohmagari Norio , Beutels Philippe 
Published: September 2021

AbstractBackgroundThe empirical basis for a quantitative assessment of the disease burden imposed by long-COVID is currently scant. We aimed to assess the disease burden caused by long-COVID in Japan.MethodsWe conducted a cross sectional self-report questionnaire survey. The questionnaire was mailed to 530 eligible patients, who were recovered from acute COVID-19 in April 2021. Answers were classified into two groups; participants who have no symptom and those who have any ongoing symptoms that lasted longer than four weeks at the time of the survey. We compared health-related quality of life scores estimated by the EQ-5D-3L questionnaire between these two groups after adjusting basic characteristics of the participants by propensity score matching.Results349 participants reported no symptoms and 108 reported any symptoms at the time of the survey. The participants who reported any symptoms showed a lower value on a Visual Analogue Scale (median 70 [IQR 60-80]) and on the EQ-5D-3L (median 0.81 [IQR 0.77-1.0]) than those reporting no symptoms (median 85 [IQR 75-90] and 1.0 [IQR 1.0-1.0], respectively). After adjusting for background characteristics, these trends did not change substantially (Visual Analog Scale: median 70 [IQR 60-80] vs 80 [IQR 77-90], EQ-5D-3L: median 0.81 [IQR 0.76-1.0] vs 1.0 [IQR 1.0-1.0]).ConclusionsDue to their long duration, long-COVID symptoms represent a substantial disease burden expressed in impact on health-related quality of life.Trial registrationNot applicable.
Rhizobial adhesives enhance nodule formation in sunn hemp
Authors: Rai Qulina , Choudhury Robin , Soti Pushpa , Racelis Alexis 
Published: September 2021

ABSTRACTInoculation of legume seed with rhizobacteria before planting is an efficient and convenient way of introducing effective rhizobacteria to soil vicinity of legume root and ensuring nitrogen fixation in cover cropped field. However, there are still challenges in identifying the proper seed coating technique to ensure microbial survival in adverse environmental conditions and maintaining the symbiotic relation with plants. The objectives of this study are firstly, to analyze the effectiveness of different sticking agents aiding inoculation of Bradyrhizobium japonicum L. in sunn hemp seeds to enhance root nodule formation. Secondly, to observe nodulation pattern over time as affected by the treatment and lastly to check if there is significant difference between main root and lateral root nodulation pattern due to the treatments. Two similar field studies were conducted in fall 2019 and summer 2020 using four sticking agents: water, peanut oil, 10% jaggery solution, and 40% gum arabic solution. The fall study showed no significant differences among total nodules across treatments, but percentage of active nodules was highest in the oil treatment and lowest in the water treatment. In the summer study, significantly higher total nodules were seen in the jaggery treatment and the lowest was in water treatment again, however, there were no differences in percentage of total active nodules across treatments. Interestingly, the trend across weeks showed gum arabic treatment exhibiting higher main root nodulation and jaggery treatment exhibiting higher lateral root nodulation. Overall, water as an adhesive was less effective in aiding nodulation compared to other treatments. Peanut oil and jaggery showed better performance as adhesives aiding active nodulation and could be more effective than gum arabic or water.