bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing
Authors: Miao Qing , Liang Tianzhu , Pei Na , Liu Chunjiao , Pan Jue , Li Na , Wang Qingqing , Chen Yanqiong , Chen Yu , Ma Yuyan , Jin Wenting , Zhang Yao , Su Yi , Yao Yumeng , Huang Yingnan , Zhou Chunmei , Bao Rong , Xu Xiaoling , Chen Weijun , Hu Bijie , Li Junhua 
Published: December 2022

Abstract
Background
The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.

Methods
Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.

Results
The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.

Conclusions
To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.
Bacillus integrative plasmid system combining a synthetic gene circuit for efficient genetic modifications of undomesticated Bacillus strains
Authors: Kim Man Su , Jeong Da-Eun , Choi Soo-Keun 
Published: December 2022

Abstract
Background
Owing to CRISPR-Cas9 and derivative technologies, genetic studies on microorganisms have dramatically increased. However, the CRISPR-Cas9 system is still difficult to utilize in many wild-type Bacillus strains owing to Cas9 toxicity. Moreover, less toxic systems, such as cytosine base editors, generate unwanted off-target mutations that can interfere with the genetic studies of wild-type strains. Therefore, a convenient alternative system is required for genetic studies and genome engineering of wild-type Bacillus strains. Because wild-type Bacillus strains have poor transformation efficiencies, the new system should be based on broad-host-range plasmid-delivery systems.

Results
Here, we developed a Bacillus integrative plasmid system in which plasmids without the replication initiator protein gene (rep) of Bacillus are replicated in a donor Bacillus strain by Rep proteins provided in trans but not in Bacillus recipients. The plasmids were transferred to recipients through a modified integrative and conjugative element, which is a wide host range plasmid-delivery system. Genetic mutations were generated in recipients through homologous recombination between the transferred plasmid and the genome. The system was improved by adding a synthetic gene circuit for efficient screening of the desired mutations by double crossover recombination in recipient strains. The improved system exhibited a mutation efficiency of the target gene of approximately 100% in the tested wild-type Bacillus strains.

Conclusion
The Bacillus integrative plasmid system developed in this study can generate target mutations with high efficiency when combined with a synthetic gene circuit in wild-type Bacillus strains. The system is free of toxicity and unwanted off-target mutations as it generates the desired mutations by traditional double crossover recombination. Therefore, our system could be a powerful tool for genetic studies and genome editing of Cas9-sensitive wild-type Bacillus strains.
Choice of health providers and health-seeking behaviour among forest goer population in Myanmar: findings from a cross-sectional household survey
Authors: Thet May Me , Khaing Myat Noe Thiri , Zin Su Su , Thein Si Thu , Tesfazghi Kemi 
Published: December 2022

Abstract
Background
In Myanmar, malaria still poses a significant burden for vulnerable populations particularly forest goers even though impressive progress has been made over the past decade. Limited evidence existed related to forest goers’ health-seeking behaviour and factors that drive decision making for providers’ choice to support national malaria programmes towards elimination. In response to that, this research is conducted to identify who they preferred and what are the factors associated with providers’ choice in malaria febrile illness and Rapid Diagnostic Testing (RDT).

Methods
A cross-sectional study applying quantitative household survey was completed with 479 forest goer households in 20 malaria endemic townships across Myanmar. The household data was collected with the types of providers that they consulted for recent and previous febrile episodes. To identify the factors associated with providers’ choices, univariate and multivariate multinomial logistic regressions were done using Stata version 14.1. Statistical significance was set as p = 0.05.

Results
A total of 307 individuals experienced fever within one month and 72.3% sought care from providers. Also, a total of 509 forest goers reported that they had a previous febrile episode and 62.6% received care from a provider. Furthermore, 56.2% said that they had RDT testing during these previous febrile illnesses. They consulted public facilities and public health staff, private facilities, private and semi-private providers, community health volunteers or workers in their residing village and those located outside their villages but majority preferred those within their villages. On multivariate analyses, second richest quintile (public, RRR = 12.9) (semi-private, RRR = 17.9), (outside, RRR = 8.4) and access to 4 and above nearby providers (public, RRR = 30.3) (semi-private, RRR = 1.5) (outside, RRR = 0.5) were found to be significantly associated with provider choice for recent fever episode. Similar findings were also found for previous febrile illness and RDT testing among forest goers.

Conclusions
It was highlighted in this study that in forest goer households, they preferred nearby providers and the decision to choose providers seemed to be influenced by their access to number of nearby providers and socio-economic status when they sought care from a provider regardless of fever occurrence location. It was important that the national programmes considere involving these nearby providers in elimination efforts.
Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure
Authors: Qu Rihao , Kluger Yuval , Yang Junchen , Zhao Jun , Hafler David A. , Krause Diane S. , Bersenev Alexey , Bosenberg Marcus , Hurwitz Michael , Lucca Liliana , Kluger Harriet M. 
Published: December 2022

AbstractAdoptive cell therapy (ACT) using tumor infiltrating lymphocytes (TIL) is being studied in multiple tumor types. However, little is known about clonal cell expansion in vitro and persistence of the ACT product in vivo. We performed single-cell RNA and T-Cell Receptor (TCR) sequencing on serial blood and tumor samples from a patient undergoing ACT, who did not respond. We found that clonal expansion varied during preparation of the ACT product, and only one expanded clone was preserved in the ACT product. The TCR of the preserved clone which persisted and remained activated for five months was previously reported as specific for cytomegalovirus and had upregulation of granzyme family genes and genes associated with effector functions (HLA-DQB1, LAT, HLA-DQA1, and KLRD1). Clones that contracted during TIL preparation had features of exhaustion and apoptosis. At disease progression, all previously detected clonotypes were detected. New clonotypes appearing in blood or tumor at disease progression were enriched for genes associated with cytotoxicity or stemness (FGFBP2, GNLY, GZMH, GZMK, IL7R, SELL and KLF2), and these might be harnessed for alternative cellular therapy or cytokine therapy. In-depth single-cell analyses of serial samples from additional ACT-treated patients is warranted, and viral- versus tumor-specificity should be carefully analyzed.
Factors associated with the speed and scope of diffusion of COVID-19 therapeutics in a nationwide healthcare setting: a mixed-methods investigation
Authors: La Jennifer , Fillmore Nathanael R. , Do Nhan V. , Brophy Mary , Monach Paul A. , Branch-Elliman Westyn 
Published: December 2022

Abstract
Background
The global COVID-19 pandemic is an opportunity to evaluate factors associated with high levels of adoption of different therapeutics in a real-world setting. The aim of this nationwide, retrospective cohort study was to evaluate the diffusion and adoption of novel therapeutics with an emerging evidence basis and to identify factors that influenced physicians’ treatment decisions.

Methods
Cohort creation: A cohort of Veteran patients with a microbiologically confirmed diagnosis of SARS-CoV2 were identified, and cases were classified by disease severity (outpatient, inpatient with mild and severe disease, intensive care unit ICU]). After classification of disease severity, the proportion of cases (outpatients) and admissions (inpatients) in each category receiving each type of medication were plotted as a function of time. Identification of milestones and guidance changes: Key medications used for the management of COVID-19 milestones in the release of primary research results in various forms (e.g. via press release, preprint or publication in a traditional medical journal), policy events and dates of key guidelines were identified and plotted as a timeline. After a timeline was created, time points were compared to changes in medication use, and factors potentially impacting the magnitude (i.e. proportion of patients who received the treatment) and the speed (i.e. the slope of the change in use) of practice changes were evaluated.

Results
Dexamethasone and remdesivir, the first two medications with clinical trial data to support their use, underwent the most rapid, complete and sustained diffusion and adoption; the majority of practice changes occurred after press releases and preprints were available and prior to guideline changes, although some additional uptake occurred following guideline updates. Medications that were not “first in class”, that were identified later in the pandemic, and that had higher perceived risk had slower and less complete uptake regardless of the strength and quality of the evidence supporting the intervention.

Conclusions
Our findings suggest that traditional and social media platforms and preprint releases were major catalysts of practice change, particularly prior to the identification of effective treatments. The “first available treatment in class” impact appeared to be the single most important factor determining the speed and scope of diffusion.
Long-term survivors demonstrate superior quality of life after haploidentical stem cell transplantation to matched sibling donor transplantation
Authors: Zhang Xiaoyu , Wang Jiao , Liu Yuqiu , Liu Jie , Wang Bei , Zhang Qiuhui , Guan Wei , Zhang Huijuan , Xu Li , Liu Guiying , Zhang Ping , He Yi , Feng Sizhou , Han Mingzhe , Li Changping , Jiang Erlie , Xie Wenjun 
Published: December 2022

Abstract
Background
It has been well-documented that haplo-identical hematopoietic stem cell transplantation (HID-HSCT) can provide outcomes comparable to conventional matched sibling donor (MSD) HSCT, however, little is known about the effects on quality of life (QoL) in long-term survivors. This study is to investigate the differences in longitudinal performance of QoL between HID and MSD HSCT using a comprehensive assessment system.

Methods
This prospective study enrolled consecutive patients who had received allogenic-HSCT (allo-HSCT) between January 2018 and December 2019 in our center. All patients were informed to complete QoL questionnaires including the Mos 36-Item Short-Form Health Survey (SF-36) and the Functional Assessment of Cancer Therapy Bone Marrow Transplant (FACT-BMT, version 4), using an online applet, before transplantation and at scheduled time points after transplantation. The linear mixed-effects model was used to analyze the variation trend of different dimensions of both SF-36 and FACT-BMT with different follow-up times.

Results
Of the 425 participants, recipients of HID and MSD who survived more than 1 year (n = 230) were included in the final analysis of QoL (median age [range]: 36, [15, 66]). The 3 year overall survival (OS) of HID and MSD was 82.42% and 86.46%, respectively. QoL was assessed using both SF-36 and FACT-BMT and there was longitudinal recovery with clinical significance in the cohort. Compared to MSD-HSCT patients, HID-HSCT recipients demonstrated superior QoL performance in some subscales describing physical and mental wellness. Specifically, the difference in physical performance is more remarkable using FACT-BMT whereas that in mental wellness is more significant using SF36. In the subsequent stratified analysis, patients with a history of aGVHD or CMV reactivation demonstrated inferior QoL.

Conclusions
Long-term survivors of HID HSCT achieved better QoL in some sub-scales compared to MSD HSCT. In addition, SF-36 and FACT-BMT demonstrated different performance thus combination of both improved capacity of the evaluation system.
Models of microglia depletion and replenishment elicit protective effects to alleviate vascular and neuronal damage in the diabetic murine retina
Authors: Church Kaira A. , Rodriguez Derek , Vanegas Difernando , Gutierrez Irene L. , Cardona Sandra M. , Madrigal José L. M. , Kaur Tejbeer , Cardona Astrid E. 
Published: December 2022

AbstractMicroglia, the resident phagocytes of the retina, are believed to influence the development of retinopathy, but their exact contributions to vascular integrity and neuronal loss are unknown. Therefore, utilizing two models of microglia depletion, we aimed to deplete and repopulate microglia to clarify the contribution of microglia to neuronal loss and vascular damage in the diabetic retina in an STZ-induced model of hyperglycemia. Here, we report that 2 weeks exposure to diphtheria toxin (DTx) in diabetic CX3CR1CreER:R26iDTR transgenic mice induced a 62% increase in Iba1+ microglia associated with an increase in TUJ1+ axonal density and prevention of NeuN+RBPMS+ neuronal loss. Conversely, diabetic PBS controls exhibited robust TUJ1+ axonal and NeuN+RBPMS+ neuronal loss compared to non-diabetic controls. A 2-week recovery period from DTx was associated with a 40% reduction in angiogenesis and an 85% reduction in fibrinogen deposition into the diabetic retina in comparison to diabetic PBS-treated controls. Analysis of microglia morphology and marker expression revealed that following a 2-week recovery period microglia displayed a P2RY12+Ly6C– phenotype and high transformation index (TI) values complimented by a ramified-surveillant morphology closely resembling non-diabetic controls. In contrast, diabetic PBS-treated control mice displayed P2RY12+Ly6C+ microglia, with a 50% reduction in TI values with an amoeboid morphology. To validate these observations were due to microglia depletion, we used PLX-5622 to assess vascular and neuronal damage in the retinas of diabetic mice. Confocal microscopy revealed that PLX-5622 also induced an increase in TUJ1+ axonal density and prevented fibrinogen extravasation into the diabetic retina. mRNAseq gene expression analysis in retinal isolates revealed that PLX-5622-induced microglia depletion and repopulation induced a downregulation in genes associated with microglial activation and phagocytosis, B2m, Cx3cr1, and Trem2, and complement-associated synaptic pruning, C1qa, C1qb, and C1qc. Although the levels of microglia depletion induced with DTx in the CX3CR1CreER:R26iDTR model and those induced with the CSF-1R antagonists are distinct, our results suggest that microglia depletion and replenishment is neuroprotective by inducing the proliferation of a homeostatic microglia pool that supports neuronal and vascular integrity.
Blood and cerebrospinal fluid flow oscillations measured with real-time phase-contrast MRI: breathing mode matters
Authors: Laganà Maria Marcella , Di Tella Sonia , Ferrari Francesca , Pelizzari Laura , Cazzoli Marta , Alperin Noam , Jin Ning , Zacà Domenico , Baselli Giuseppe , Baglio Francesca 
Published: December 2022

Abstract
Background
Cervical blood and cerebrospinal fluid (CSF) flow rates can be quantified with Phase-contrast (PC) MRI, which is routinely used for clinical studies. Previous MRI studies showed that venous and CSF flow alterations are linked to various pathological conditions. Since it is well known that, besides the heart beating, the thoracic pump influences the blood and CSF dynamics, we studied the effect of different respiration modes on blood and CSF flow rates using a real-time (RT)-PC prototype.

Methods
Thirty healthy volunteers were examined with a 3 T scanner. A RT-PC sequence was acquired at the first cervical level to quantify the flow rates of internal carotid arteries, internal jugular veins (IJVs) and CSF. Each RT-PC acquisition was repeated three times, while the subjects were asked to breathe in three different ways for 60 s each: freely (F), with a constant rate (PN) and with deep and constant respiration rate (PD). The average flow rates were computed, they were removed from the respective signals and integrated in the inspiratory and expiratory phases (differential volumes). Finally, the power spectral density was computed for each detrended flow rate. High- and very-high frequency peaks were identified on the spectra while their frequencies were compared to the respiratory and cardiac frequencies estimated using a thoracic belt and a pulse oximeter. The area under the spectra was computed in four 0.5 Hz-wide ranges, centered on the high-frequency peak, on very-high frequency peak and its 2nd and 3rd harmonics, and then they were normalized by the flow rate variance. The effect of breathing patterns on average flow rates, on systolic and diastolic peaks, and on the normalized power was tested. Finally, the differential volumes of inspiration were compared to those of expiration.

Results
The frequencies of the high- and very-high spectral peaks corresponded to the respiratory and cardiac frequencies. The average flow rate progressively decreased from F to PN to PD breathing, and the cardiac modulations were less predominant especially for the IJVs. The respiratory modulation increased with PD breathing. The average volumes displaced in the inspiratory phases were not significantly different from those of the expiratory one.

Conclusions
The spectral analyses demonstrated higher respiratory modulations in PD compared to free breathing, even prevailing the cardiac modulation in the IJVs, showing an increment of the thoracic pump affecting the flow rate shape.
Analysis and mapping of global research publications on shift work (2012–2021)
Authors: Sweileh Waleed M. 
Published: December 2022

Abstract
Background
The main objective of the study was to identify research trends, collaboration patterns, and the most impactful publications in the field of shift work.

Methods
Documents published in scientific journals indexed in the Scopus database on shift work were retrieved and analyzed using the title/abstract search methodology. The study period was from January 1st, 2012, to December 31st, 2021.

Results
Two thousand three hundred twenty-eight documents were retrieved with an h-index of 71 and an average number of 4.5 authors per document. The cumulative number of publications showed a linear growth pattern, while that of citations showed an exponential pattern. The most frequent author keywords, excluding keywords related to shift work, were sleep, fatigue, and nursing. The average annual growth rate was 4.3, and the average doubling time was 3.2. No significant correlation was found between the number of publications and national income among prolific countries. Cross-country research collaboration was weak while the degree of author-author collaboration was relatively high. The Chronobiology International journal was the most prolific, while Harvard University was the most active institution in the field of shift work.

Conclusions
Given the volume and the negative health impact of shift work, better human resource management is needed to create safer and healthier working schedules.
Pseudo high-frequency boosts the generalization of a convolutional neural network for cassava disease detection
Authors: Zhang Jiayu , Qi Chao , Mecha Peter , Zuo Yi , Ben Zongyou , Liu Haolu , Chen Kunjie 
Published: December 2022

AbstractFrequency is essential in signal transmission, especially in convolutional neural networks. It is vital to maintain the signal frequency in the neural network to maintain the performance of a convolutional neural network. Due to destructive signal transmission in convolutional neural network, signal frequency downconversion in channels results into incomplete spatial information. In communication theory, the number of Fourier series coefficients determines the integrity of the information transmitted in channels. Consequently, the number of Fourier series coefficients of the signals can be replenished to reduce the information transmission loss. To achieve this, the ArsenicNetPlus neural network was proposed for signal transmission modulation in detecting cassava diseases. First, multiattention was used to maintain the long-term dependency of the features of cassava diseases. Afterward, depthwise convolution was implemented to remove aliasing signals and downconvert before the sampling operation. Instance batch normalization algorithm was utilized to keep features in an appropriate form in the convolutional neural network channels. Finally, the ArsenicPlus block was implemented to generate pseudo high-frequency in the residual structure. The proposed method was tested on the Cassava Datasets and compared with the V2-ResNet-101, EfficientNet-B5, RepVGG-B3g4 and AlexNet. The results showed that the proposed method performed $$95.93\%$$

95.93
%

in terms of accuracy, 1.2440 in terms of loss, and $$95.94\%$$

95.94
%

in terms of the F1-score, outperforming the comparison algorithms.