bluuebunny/crossref_metadata_2025_split huggingface dataset:
People living with HIV easily lose their immune response to SARS-CoV-2: result from a cohort of COVID-19 cases in Wuhan, China
Authors: Liu Yanbin , Xiao Yanling , Wu Songjie , Marley Gifty , Ming Fangzhao , Wang Xiaoya , Wu Mengmeng , Feng Ling , Tang Weiming , Liang Ke 
Published: October 2021

Abstract
Background
To date, whether the immune response for SARS-CoV-2 infection among people living with HIV(PLWH) is different from HIV-naïve individuals is still not clear.

Methods
In this cohort study, COVID-19 patients admitted to hospitals in Wuhan between January 15 and April 1, 2020, were enrolled. Patients were categorized into PLWH and HIV-naïve group. All patients were followed up regularly (every 15 days) until November 30, 2020, and the immune response towards SARS-CoV-2 was observed.

Results
Totally, 18 PLWH and 185 HIV-naïve individuals with COVID-19 were enrolled. The positive conversion rates of IgG were 56% in PLWH and 88% in HIV-naïve patients respectively, and the peak was on the 45th day after COVID-19 onset. However, the positive rate of IgG dropped to 12% in PLWH and 33% among HIV-naïve individuals by the end of the study. The positive conversion rate of IgG among asymptomatic carriers is significantly lower than that among patients with moderate disease (AOR = 0.24, 95% CI 0.07–0.85). PLWH had a lower IgG seroconversion rate (AOR = 0.11, 95% CI 0.03–0.39) and shorter IgG duration (AHR = 3.99, 95% CI 1.43–11.13) compared to HIV-naïve individuals. Patients with higher lymphocyte counts at onset had a lower positive conversion rate (AOR = 0.30, 95% CI 0.10–0.87) and shorter duration for IgG (AHR = 4.01, 95% CI 1.78–9.02).

Conclusions
The positive conversion rate of IgG for SARS-CoV-2 was relatively lower and quickly lost in PLWH.
Genotypic and phenotypic characteristics of Streptococcus pneumoniae from community-acquired pneumonia patients and healthy asymptomatic participants in Sichuan province, China
Authors: Peng Shihui , Ren Hongyu , Deng Jianping , Zhao Na , Li Yinan , Li Ming , Yuan Qiwu , Zhang Zhengdong , Luo Longze , Zeng Linzi , Wang Bin , Zou Nianli , Gu Changguo , Huang Xin , Liao Zheng , Chen Shenen , Chen Haiying , Li Qun , Qin Tian 
Published: October 2021

Abstract
Background
Streptococcus pneumoniae (S. pneumoniae) is the common cause of community-acquired pneumonia (CAP) and is also found in the upper respiratory tract of healthy people. Hence, the study aimed to compare the serotypes, virulence/pili genes, and antibiotic susceptibility of S. pneumoniae from healthy asymptomatic participants and CAP patients.

Methods
Streptococcus pneumoniae were retrospectively collected from health asymptomatic participants and CAP patients in Sichuan, China. The serotypes were tested by multiplex polymerase chain reaction (PCR) or Quellung reaction. Antibiotic susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S. pneumoniae was analyzed by multilocus sequence typing (MLST). Additionally, the presence of virulence/pili genes were detected using PCR.

Results
A total of 83 pneumococcal isolates were collected in the current study. Of these, 52 and 31 isolates were from healthy asymptomatic participants and CAP patients, respectively. Most of S. pneumoniae were resistant to erythromycin (ERY), clindamycin (CLI), tetracycline (TET) and trimethoprim-sulfamethoxazole (SXT). 90.4% isolates were classified as multidrug resistant (MDR). The predominant serotypes were 3, 19F and 19A in the CAP carriers, whereas 3, 6 and 19F were the main serotypes among the asymptomatic carriers. The overall coverage rates of pneumococcal conjugate vaccine (PCV) 10 and PCV13 serotypes were 34.9% and 66.3%, respectively. The predominant sequence types (STs) were ST271, ST320, and ST3397. There were significant differences in some resistance and virulence characteristics between CAP patients and asymptomatic carriers. Additionally, clonal complex (CC) 271 strains had higher percentage in resistance to cefuroxime (CXM) and cefotaxime (CEF), meropenem (MER) and cefepime (CFP), which mainly carried the rlrA and sipA genes.

Conclusions
High coverage rate of PCV13 and high prevalence of MDR indicated the necessity to expand immunization with PCV13 and rationally use the antibiotics in Sichuan, China. Importantly, long-term surveillance should be conducted to assess effectiveness brought by vaccines. Our findings may supply new guidance for developing new pneumococcal vaccines.
Factors associated with the use of complementary therapies in Taiwanese patients with systemic lupus erythematosus: a cross-sectional study
Authors: Lu Ming-Chi , Lo Hui-Chin , Chang Hsiu-Hua , Hsu Chia-Wen , Koo Malcolm 
Published: October 2021

Abstract
Background
This study aimed to investigate the prevalence of and the factors associated with the regular use of complementary therapies for Taiwanese patients with systemic lupus erythematosus (SLE).

Methods
In this cross-sectional study, 351 patients with SLE were consecutively recruited from a regional hospital in southern Taiwan from April to August 2019. Demographic and clinical information, including the use of different types of complementary therapies, was ascertained using a self-constructed questionnaire. Disease-specific quality of life was measured using the Lupus Quality of Life (LupusQoL) questionnaire. SLE disease activity was assessed using the rheumatologist-scored Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2 K). Factors associated with the regular use of complementary therapies were evaluated using multiple logistic regression analyses.

Results
Of the 351 patients with SLE, 90.3% were female, and 60.1% were ≥ 40 years of age. The prevalence of the regular use of any type of complementary therapy was 85.5%. The five most popular types of complementary therapy used were (1) fitness walking or strolling, (2) Buddhist prayer or attending temple, (3) vitamin consumption, (4) calcium supplementation, and (5) fish oil supplementation. Multiple logistic regression analyses revealed that the significant and independent factors associated with the regular use of complementary therapies in patients with SLE were age ≥ 40 years (adjusted odds ratio [aOR] 2.76, p = 0.013), nonoverweight or nonobesity (aOR 0.29, p = 0.004), engagement in vigorous exercise in the past year (aOR 4.62, p = 0.002), a lower SLEDAI-2 K score (aOR 0.90, p = 0.029), and a lower score in the physical health domain of the LupusQoL (aOR 0.57, p = 0.001).

Conclusions
A high prevalence of complementary therapy use in Taiwanese patients with SLE was observed. Rheumatologists should routinely ask patients about their use of supplements to minimize the risk of interaction with medical therapy.
Potential antiviral effects of some native Iranian medicinal plants extracts and fractions against influenza A virus
Authors: Mehrbod Parvaneh , Safari Hanieh , Mollai Zeinab , Fotouhi Fatemeh , Mirfakhraei Yasaman , Entezari Hanieh , Goodarzi Saied , Tofighi Zahra 
Published: October 2021

Abstract
Background
Influenza A virus (IAV) infection is a continual threat to the health of animals and humans globally. Consumption of the conventional drugs has shown several side effects and drug resistance. This study was aimed to screen some Iranian medicinal plants extracts and their fractions against influenza A virus.

Methods
Glycyrrhiza glabra (rhizome), Myrtus  commonis (leaves), Melissa officinalis (leaves), Hypericum perforatum (aerial parts), Tilia platyphyllos (flower), Salix alba (bark), and Camellia sinensis (green and fermented leaves) were extracted with 80% methanol and fractionated with chloroform and methanol, respectively. The cytotoxicity of the compounds were determined by MTT colorimetric assay on MDCK cells. The effective concentrations (EC50) of the compounds were calculated from the MTT results compared to the negative control with no significant effects on cell viability. The effects of EC50 of the compounds on viral surface glycoproteins and viral titer were tested by HI and HA virological assays, respectively and compared with oseltamivir and amantadine. Preliminary phytochemical analysis were done for promising anti-IAV extracts and fractions.

Results
The most effective samples against IAV titer (P ≤ 0.05) were crude extracts of G. glabra, M. officinalis and S. alba; methanol fractions of M. communis and M. officinalis; and chloroform fractions of M. communis and C. sinensis (fermented) mostly in co- and pre-penetration combined treatments. The potential extracts and fractions were rich in flavonoids, tannins, steroids and triterpenoids.

Conclusion
The outcomes confirmed a scientific basis for anti-influenza A virus capacity of the extracts and fractions from the selected plants for the first time, and correlated their effects with their phytochemical constituents. It is worth focusing on elucidating pure compounds and identifying their mechanism(s) of action.
Pharmacogenetics: Knowledge assessment amongst Syrian pharmacists and physicians
Authors: Albitar Lina , Alchamat Ghalia Abou 
Published: October 2021

Abstract
Background
Pharmacogenetics targets genetic variations that influence drug response. It is relatively a new science that has not been vastly employed in most developing countries including Syria. Therefore we aimed at evaluating the depth of knowledge in pharmacogenetics and the attitude towards it amongst Syrian pharmacists and physicians.

Methods
We carried out an internet-based questionnaire consisted of 26 questions, sent through specialized websites and private groups with a large number of pharmacists and physicians members. The survey was available online for a period of 1 month.

Results
The total number of respondents was 154, mostly female pharmacists. Our statistical analysis showed a strong positive association between profession (in favour of pharmacists) and pharmacogenetics knowledge p = 0.049; however, no correlation with experience p = 0.811 was found. A significant difference was reported between the knowledge of pharmacists and physicians p = 0.001 concerning drugs that need pharmacogenetics testing before being prescribed. The majority of respondents had no information about applying genetic tests in Syria before prescribing medications nor did they possess the knowledge regarding drugs that show differential responses in patients according to their unique genotypes. In our study, the percentage knowledge assessment score was low in general (mean ± Standard deviation, SD) (46% ± 13.9%). The majority of the respondents agreed that pharmacists should provide counselling to patients on the subject of pharmacogenetics. Respondents’ opinions varied concerning making pharmacogenetics learning a priority.

Conclusion
Lack of pharmacogenetics knowledge was found amongst respondents in general. Our findings raise concerns about the lack of awareness amongst physicians, which may hinder the implementation of this crucial field in Syria. We suggest an emphasis on the role of education, training, and conducting genotyping research on the Syrian population.
Causes of multidrug-resistant tuberculosis from the perspectives of health providers: challenges and strategies for adherence to treatment during the COVID-19 pandemic in Brazil
Authors: Souza Ludmilla Leidianne Limirio , Santos Felipe Lima dos , Crispim Juliane de Almeida , Fiorati Regina Célia , Dias Sónia , Bruce Alexandre Tadashi Inomata , Alves Yan Mathias , Ramos Antônio Carlos Vieira , Berra Thaís Zamboni , da Costa Fernanda Bruzadelli Paulino , Alves Luana Seles , Monroe Aline Aparecida , Fronteira Inês , Arcêncio Ricardo Alexandre 
Published: October 2021

Abstract
Background
Multidrug-resistant tuberculosis (MDR-TB) is a serious phenomenon on a global scale that can worsen with the COVID-19 pandemic. The study aimed to understand the perceptions of health professionals about MDR-TB, their strategies to ensure adherence to treatment and their challenges in the context of the COVID-19 pandemic in a priority municipality for disease control.

Methods
We conducted a qualitative study and recruited 14 health providers (four doctors, three nurses, three nursing technicians, three nursing assistants and a social worker) working in a city in the state of São Paulo, Brazil. Remote semi-structured interviews were conducted with the participants. For data analysis, the thematic content analysis technique was applied according to the study’s theoretical framework.

Results
The study revealed the causes of MDR-TB are associated with poverty, vulnerability, and social risk. A pre-judgement from the providers was observed, namely, all patients do not adhere due their resistance and association with drug abuse or alcoholism. The study also observed difficulty among health providers in helping patients reconstruct and reframe their life projects under a care perspective, which would strengthen adherence. Other issues that weakened adherence were the cuts in social protection and the benefits really necessary to the patients and a challenge for the providers manage that. The participants revealed that their actions were impacted by the pandemic and insecurity and fear manifested by patients after acquiring COVID-19. For alleviating this, medical appointments by telephone, delivery of medicine in the homes of patients and visits by health professionals once per week were provided.

Conclusion
The study advances knowledge by highlighting the challenges faced by the health system with the adherence of patients with MDR-TB in a context aggravated by the pandemic. An improvement in DOT is really necessary to help the patients reframe their lives without prejudices, face their fears and insecurity, recover their self-esteem and motivate in concluding their treatment.
Comparison of Scanpy-based algorithms to remove the batch effect from single-cell RNA-seq data
Authors: Li Jiaqi , Yu Chengxuan , Ma Lifeng , Wang Jingjing , Guo Guoji 
Published: October 2021

AbstractWith the development of single-cell RNA sequencing (scRNA-seq) technology, analysts need to integrate hundreds of thousands of cells with multiple experimental batches. It is becoming increasingly difficult for users to select the best integration methods to remove batch effects. Here, we compared the advantages and limitations of four commonly used Scanpy-based batch-correction methods using two representative and large-scale scRNA-seq datasets. We quantitatively evaluated batch-correction performance and efficiency. Furthermore, we discussed the performance differences among the evaluated methods at the algorithm level.
The cellular niche for intestinal stem cells: a team effort
Authors: Zhu Guoli , Hu Jiulong , Xi Rongwen 
Published: October 2021

AbstractThe rapidly self-renewing epithelium in the mammalian intestine is maintained by multipotent intestinal stem cells (ISCs) located at the bottom of the intestinal crypt that are interspersed with Paneth cells in the small intestine and Paneth-like cells in the colon. The ISC compartment is also closely associated with a sub-epithelial compartment that contains multiple types of mesenchymal stromal cells. With the advances in single cell and gene editing technologies, rapid progress has been made for the identification and characterization of the cellular components of the niche microenvironment that is essential for self-renewal and differentiation of ISCs. It has become increasingly clear that a heterogeneous population of mesenchymal cells as well as the Paneth cells collectively provide multiple secreted niche signals to promote ISC self-renewal. Here we review and summarize recent advances in the regulation of ISCs with a main focus on the definition of niche cells that sustain ISCs.
Vertebrate cardiac regeneration: evolutionary and developmental perspectives
Authors: Cutie Stephen , Huang Guo N. 
Published: October 2021

AbstractCardiac regeneration is an ancestral trait in vertebrates that is lost both as more recent vertebrate lineages evolved to adapt to new environments and selective pressures, and as members of certain species developmentally progress towards their adult forms. While higher vertebrates like humans and rodents resolve cardiac injury with permanent fibrosis and loss of cardiac output as adults, neonates of these same species can fully regenerate heart structure and function after injury – as can adult lower vertebrates like many teleost fish and urodele amphibians. Recent research has elucidated several broad factors hypothesized to contribute to this loss of cardiac regenerative potential both evolutionarily and developmentally: an oxygen-rich environment, vertebrate thermogenesis, a complex adaptive immune system, and cancer risk trade-offs. In this review, we discuss the evidence for these hypotheses as well as the cellular participators and molecular regulators by which they act to govern heart regeneration in vertebrates.
Activation of the Melanocortin-4 receptor signaling by α-MSH stimulates nerve-dependent mouse digit regeneration
Authors: Xu Hanqian , Zhang Hailin , Fang Yanqing , Yang Huiran , Chen Ying , Zhang Chao , Lin Gufa 
Published: October 2021

Abstract
Background
Expression of Mc4r in peripheral organs indicates it has broader roles in organ homeostasis and regeneration. However, the expression and function of Mc4r in the mouse limb and digit has not been fully investigated. Our previous work showed that Mc4r−/− mice fail to regenerate the digit, but whether activation of MC4R signaling could rescue digit regeneration, or stimulate proximal digit regeneration is not clear.

Results
We analyzed the expression dynamics of Mc4r in the embryonic and postnatal mouse limb and digit using the Mc4r-gfp mice. We found that Mc4r-GFP is mainly expressed in the limb nerves, and in the limb muscles that are undergoing secondary myogenesis. Expression of Mc4r-GFP in the adult mouse digit is restricted to the nail matrix. We also examined the effect of α-MSH on mouse digit regeneration. We found that administration of α-MSH in the Mc4r+/− mice rescue the delayed regeneration of distal digit tip. α-MSH could rescue distal digit regeneration in denervated hindlimbs. In addition, α-MSH could stimulate regeneration of the proximally amputated digit, which is non-regenerative.

Conclusions
Mc4r expression in the mouse limb and digit is closely related to nerve tissues, and α-MSH/MC4R signaling has a neurotrophic role in mouse digit tip regeneration.
Organoid: a powerful tool to study lung regeneration and disease
Authors: Lu Tiantian , Cao Yiyuan , Zhao Peng , Shen Shengxi , Xi Ying 
Published: October 2021

AbstractOrganoids are three-dimensional self-organizing structures formed by adult tissue stem cells or pluripotent stem cells. They recapitulate cell-cell, cell-niche interactions in tissue development, homeostasis, regeneration and disease, and provide an in vitro model for drug screening. This review summarizes the recent advances of organoid cultures derived from adult lung stem cells and human pluripotent stem cells, especially focusing on the organoids of the distal airway stem/progenitor cells. We also discuss the applications of organoids in studying lung regeneration and pulmonary diseases, including pulmonary fibrosis, airway diseases and Coronavirus disease 2019 (COVID-19).
Single cells and transposable element heterogeneity in stem cells and development
Authors: Hutchins Andrew P. 
Published: October 2021

AbstractRecent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underutilized in single cell studies. One aspect is the expression and activity of transposable elements (TEs). TEs are selfish sequences of DNA that can replicate, and have been wildly successful in colonizing genomes. However, most TEs are mutated, fragmentary and incapable of transposition, yet they are actively bound by multiple transcription factors, host complex patterns of chromatin modifications, and are expressed in mRNAs as part of the transcriptome in both normal and diseased states. The contribution of TEs to development and cellular function remains unclear, and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells, development and human disease.
Deciphering and reconstitution of positional information in the human brain development
Authors: Wang Yi-Fan , Liu Cong , Xu Peng-Fei 
Published: October 2021

AbstractOrganoid has become a novel in vitro model to research human development and relevant disorders in recent years. With many improvements on the culture protocols, current brain organoids could self-organize into a complicated three-dimensional organization that mimics most of the features of the real human brain at the molecular, cellular, and further physiological level. However, lacking positional information, an important characteristic conveyed by gradients of signaling molecules called morphogens, leads to the deficiency of spatiotemporally regulated cell arrangements and cell–cell interactions in the brain organoid development. In this review, we will overview the role of morphogen both in the vertebrate neural development in vivo as well as the brain organoid culture in vitro, the strategies to apply morphogen concentration gradients in the organoid system and future perspectives of the brain organoid technology.
Coordination of EZH2 and SOX2 specifies human neural fate decision
Authors: Zhao Yuan , Wang Tianyu , Zhang Yanqi , Shi Liang , Zhang Cong , Zhang Jingyuan , Yao Jiao , Chen Qianyu , Zhong Xiaofen , Wei Yanxing , Shan Yongli , Pan Guangjin 
Published: October 2021

AbstractPolycomb repressive complexes (PRCs) are essential in mouse gastrulation and specify neural ectoderm in human embryonic stem cells (hESCs), but the underlying molecular basis remains unclear. Here in this study, by employing an array of different approaches, such as gene knock-out, RNA-seq, ChIP-seq, et al., we uncover that EZH2, an important PRC factor, specifies the normal neural fate decision through repressing the competing meso/endoderm program. EZH2−/− hESCs show an aberrant re-activation of meso/endoderm genes during neural induction. At the molecular level, EZH2 represses meso/endoderm genes while SOX2 activates the neural genes to coordinately specify the normal neural fate. Moreover, EZH2 also supports the proliferation of human neural progenitor cells (NPCs) through repressing the aberrant expression of meso/endoderm program during culture. Together, our findings uncover the coordination of epigenetic regulators such as EZH2 and lineage factors like SOX2 in normal neural fate decision.