bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying CCR5 coreceptor populations permissive for HIV-1 entry and productive infection: implications for in vivo studies
Authors: Weichseldorfer Matthew , Tagaya Yutaka , Reitz Marvin , DeVico Anthony L. , Latinovic Olga S. 
Published: January 2022

Abstract
Background
The chemokine receptor CCR5 is the major coreceptor for HIV-1 cell entry. We previously observed that not all CCR5 mAbs reduce HIV-1 infection, suggesting that only some CCR5 populations are permissive for HIV-1 entry. This study aims to better understand the relevant conformational states of the cellular coreceptor, CCR5, involved in HIV entry. We hypothesized that CCR5 assumes multiple configurations during normal cycling on the plasma membrane, but only particular forms facilitate HIV-1 infection.

Methods
To this end, we quantified different CCR5 populations using six CCR5 monoclonal antibodies (mAbs) with different epitope specificities and visualized them with super-resolution microscopy. We quantified each surface CCR5 population before and after HIV-1 infection.

Results
Based on CCR5 conformational changes, down-modulation, and trafficking rates (internalization and recycling kinetics), we were able to distinguish among heterogeneous CCR5 populations and thus which populations might best be targeted to inhibit HIV-1 entry. We assume that a decreased surface presence of a particular CCR5 subpopulation following infection means that it has been internalized due to HIV-1 entry, and that it therefore represents a highly relevant target for future antiviral therapy strategies. Strikingly, this was most true for antibody CTC8, which targets the N-terminal region of CCR5 and blocks viral entry more efficiently than it blocks chemokine binding.

Conclusions
Defining the virus-host interactions responsible for HIV-1 transmission, including specific coreceptor populations capable of establishing de novo infections, is essential for the development of an HIV-1 vaccine. This study hopefully will facilitate further development of inhibitors to block CCR5 usage by HIV-1, as well as inform future HIV-1 vaccine design.
Sleep EEG characteristics associated with total sleep time misperception in young adults: an exploratory study
Authors: Xu Biyun , Cai Qinghao , Mai Runru , Liang Hailong , Huang Jiayu , Yang Zhimin 
Published: January 2022

Abstract
Background
Power spectral analysis (PSA) is one of the most commonly-used EEG markers of cortical hyperarousal, and can help to understand subjective–objective sleep discrepancy (SOD). Age is associated with decreased sleep EEG activity; however, the PSA of young adults is currently limited. Thus, this study aimed to examine the correlation of spectral EEG power with total sleep time (TST) misperception in young patients.

Methods
Forty-seven young adults were recruited and underwent a polysomnography recording in a sleep laboratory. Clinical records and self-report questionnaires of all patients were collected, and were used to categorize patients into a good sleeper (GS) group (n = 10), insomnia with a low mismatch group (IWLM, n = 19) or participant with a high mismatch group (IWHM, n = 18). PSA was applied to the first 6 h of sleep.

Results
IWHM patients exhibited a higher absolute power and relative beta/delta ratio in the frontal region compared to the GS group. No significant difference was observed between the IWLM and GS groups. No significant difference in the above parameters was observed between the IWHM and IWLM groups. Moreover, The SOD of TST was positively correlated with frontal absolute power and the relative beta/delta ratio (r = 0.363, P = 0.012; r = 0.363, P = 0.012), and absolute beta EEG spectral power (r = 0.313, P = 0.032) as well as the number of arousals.

Conclusions
Increased frontal beta/delta ratio EEG power was found in young patients with a high mismatch but not in those with a low mismatch, compared with good sleepers. This suggests that there exists increased cortical activity in IWHM patients. In addition, the frontal beta/delta ratio and the number of arousals was positively correlated with the SOD of TST.
Monte Carlo simulation of tilted contact plaque brachytherapy placement for juxtapapillary retinoblastoma
Authors: Nakamura Satoshi , Murakami Naoya , Suzuki Shigenobu , Ito Kimiteru , Takemori Mihiro , Nakayama Hiroki , Kaga Keita , Chiba Takahito , Iijima Kotaro , Takahashi Kana , Goka Tomonori , Itami Jun , Okamoto Hiroyuki , Igaki Hiroshi 
Published: January 2022

Abstract
Background
The 106-Ruthenium contact plaque applicator is utilized for the treatment of intraocular tumor within a thickness of less than 6 mm. If anything obstructs the placement of the plaque applicator, the treatment is generally difficult because the applicator has to be temporarily located just on the opposite side of the retinal tumor. Furthermore, the plaque applicator edge of approximately 1 mm does not contain 106Ru, estimating the delivered radiation dose for eccentric tumor is challenging because the lateral dose profile is inadequately provided by the manufacture’s certification. This study aims to simulate tumor coverage of the tilted applicator placement for treating an infant with juxtapapillary retinoblastoma and to achieve the effective treatment.

Case presentation
We present an infant with retinoblastoma whose tumor involved macular and was invading just temporal side of the optic disc. Additionally, posterior staphyloma was induced by a series of previous treatments, making it more difficult to treat the standard plaque placement. Thus, the applicator type of CCA was intentionally tilted to the eyeball and the distance between the posterior edge of the applicator and the eyeball had to be then equal to or more than 2 mm based on the dose distribution of the applicator calculated using Monte Carlo simulation to minimize damage to surrounding tissues while covering the tumor. It was then comparable to the certification and previous reports. Based on the acquired dose distribution, the optimal placement of the applicator was derived from varying the distance between the applicator’s edge and the eyeball, and the distance was then determined to be 2 mm. In this case, the minimum dose rate in the tumor was 25.5 mGy/min, and the time required to deliver the prescribed dose was 26.2 h. Therefore, the tilted 106Ru plaque applicator placement could deliver the required dose for the treatment. The physical examination revealed no active tumor as a result of the treatment.

Conclusions
Optimizing the placement of the 106Ru plaque applicator, it was possible to guarantee that the prescribed dose will be delivered to the tumor even if the standard placement is not possible for the juxtapapillary tumor.
Therapy strategies of fifth metatarsal base fracture with lateral collateral ligament injury
Authors: Cao Hongbin , Li Nan , Wang Guixin , He Jinquan 
Published: January 2022

Abstract
Background
Fifth metatarsal base fracture (fifth MBF) and lateral collateral ankle ligament (LCAL) injury are mainly caused by plantar flexion and inversion of the foot. However, there is no relevant report on the incidence, injury type and treatment principle of the fifth MBF combined with an LCAL injury.

Materials and methods
We retrospectively analyzed 61 patients with fifth MBF. After admission, patients were given the symptomatic treatment and underwent standard anteroposterior (AP), 30-degree oblique foot radiographs, ankle MR and/or ultrasonic examination. The type of surgery varied base on the individual patients (type of fracture with/without lateral collateral ankle ligament injury).

Results
In 61 patients, there were 39 patients with LCAL injury. Among the 39 patients with LCAL injury, 24 patients with Grade I–II injury, 6 patients with Grade III injury, and 9 patients with avulsion fractures. There was no significant difference between the patients without LCAL injury and the patients with LCAL injury in terms of age (p = 0.67) and gender (p = 0.575). The incidence of fifth MBF with LCAL injury accounted for 63.93% of fifth metatarsal base fracture; the most common causes of injury included sprains and falls. The average fracture healing time was 8.3 (range, 6–12) weeks. For fifth MBF with displaced more than 2 mm, hook plate or lag screw was used for fixation; for complete rupture of LCAL, suture anchor was used to repairing the ligament; for partial LCAL injury, plaster was used for fixation after surgery; for avulsion fractures, cannulated screw or suture anchor was used for repair. None of the patients had complications such as delayed union, nonunion, and incision infection.

Conclusion
Early diagnosis and appropriate treatment can obtain good therapeutic results in fifth MBF patients combined with LCAL injury. Moreover, defining a treatment plan for ligament injury is essential for reducing postoperative complications. This study provides a basis for epidemiology, diagnosis, and treatment of fifth MBF with LCAL injury.
Blood-based biomarkers of inflammation in amyotrophic lateral sclerosis
Authors: Staats Kim A. , Borchelt David R. , Tansey Malú Gámez , Wymer James 
Published: January 2022

AbstractAmyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease in which many processes are detected including (neuro)inflammation. Many drugs have been tested for ALS in clinical trials but most have failed to reach their primary endpoints. The development and inclusion of different types of biomarkers in diagnosis and clinical trials can assist in determining target engagement of a drug, in distinguishing between ALS and other diseases, and in predicting disease progression rate, drug responsiveness, or an adverse event. Ideally, among other characteristics, a biomarker in ALS correlates highly with a disease process in the central nervous system or with disease progression and is conveniently obtained in a peripheral tissue. Here, we describe the state of biomarkers of inflammation in ALS by focusing on peripherally detectable and cellular responses from blood cells, and provide new (combinatorial) directions for exploration that are now feasible due to technological advancements.
IDEAS: individual level differential expression analysis for single-cell RNA-seq data
Authors: Zhang Mengqi , Liu Si , Miao Zhen , Han Fang , Gottardo Raphael , Sun Wei 
Published: January 2022

AbstractWe consider an increasingly popular study design where single-cell RNA-seq data are collected from multiple individuals and the question of interest is to find genes that are differentially expressed between two groups of individuals. Towards this end, we propose a statistical method named IDEAS (individual level differential expression analysis for scRNA-seq). For each gene, IDEAS summarizes its expression in each individual by a distribution and then assesses whether these individual-specific distributions are different between two groups of individuals. We apply IDEAS to assess gene expression differences of autism patients versus controls and COVID-19 patients with mild versus severe symptoms.
A randomized double-blind cross-over trial to study the effects of resistant starch prebiotic in chronic kidney disease (ReSPECKD)
Authors: Shamloo Maryam , Mollard Rebecca , Wang Haizhou , Kingra Kulwant , Tangri Navdeep , MacKay Dylan 
Published: January 2022

Abstract
Background
Chronic kidney disease (CKD) is associated with a reduced quality of life and an increased risk of kidney failure, cardiovascular events, and all-cause mortality. Accumulation of nitrogen-based uremic toxins leads to worsening of symptoms in individuals with CKD. Many uremic toxins, such as indoxyl and p-cresol sulphate, are produced exclusively by the gut microbiome through the proteolytic digestion of aromatic amino acids. Strategies to reduce the production of these toxins by the gut microbiome in individuals with CKD may lessen symptom burden and delay the onset of dialysis. One such strategy is to change the overall metabolism of the gut microbiome so that less uremic toxins are produced. This can be accomplished by manipulating the energy source available to the microbiome. Fermentable carbohydrates which reach the gut microbiome, like resistant starch (RS), have been shown to inhibit or reduce bacterial amino acid metabolism. This study aims to investigate the effects of resistant potato starch (RPS) as a prebiotic in individuals with CKD before the onset of dialysis.

Methods
This is a double-blind, randomized two-period crossover trial. Thirty-six eligible participants will consent to follow a 26-week study regimen. Participants will receive 2 sachets per day containing either 15 g of RPS (MSPrebiotic, resistant potato starch treatment) or 15 g cornstarch (Amioca TF, digestible starch control). Changes in blood uremic toxins will be investigated as the primary outcome. Secondary outcomes include the effect of RPS consumption on symptoms, quality of life and abundance, and diversity and functionality of the gut microbiome.

Discussion
This randomized trial will provide further insight into whether the consumption of RPS as a prebiotic will reduce uremic toxins and symptoms in individuals who have CKD.

Trial registration
ClinicalTrials.govNCT04961164. Registered on 14 July 2021
Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer
Authors: Hu Xinlei , Luo Kai , Shi Hui , Yan Xiaoqin , Huang Ruichen , Zhao Bi , Zhang Jun , Xie Dan , Zhang Wei 
Published: January 2022

Abstract
Background
Lung cancer is one of most common cancers worldwide, with a 5-year survival rate of less than 20%, which is mainly due to late-stage diagnosis. Noninvasive methods using 5-hydroxymethylation of cytosine (5hmC) modifications and fragmentation profiles from 5hmC cell-free DNA (cfDNA) sequencing provide an opportunity for lung cancer detection and management.

Results
A total of 157 lung cancer patients were recruited to generate the largest lung cancer cfDNA 5hmC dataset, which mainly consisted of 62 lung adenocarcinoma (LUAD), 48 lung squamous cell carcinoma (LUSC) and 25 small cell lung cancer (SCLC) patients, with most patients (131, 83.44%) at advanced tumor stages. A 37-feature 5hmC model was constructed and validated to distinguish lung cancer patients from healthy controls, with areas under the curve (AUCs) of 0.8938 and 0.8476 (sensitivity = 87.50% and 72.73%, specificity = 83.87% and 80.60%) in two distinct validation sets. Furthermore, fragment profiles of cfDNA 5hmC datasets were first explored to develop a 48-feature fragmentation model with good performance (AUC = 0.9257 and 0.822, sensitivity = 87.50% and 78.79%, specificity = 80.65% and 76.12%) in the two validation sets. Another diagnostic model integrating 5hmC signals and fragment profiles improved AUC to 0.9432 and 0.8639 (sensitivity = 87.50% and 83.33%, specificity = 90.30% and 77.61%) in the two validation sets, better than models based on either of them alone and performing well in different stages and lung cancer subtypes. Several 5hmC markers were found to be associated with overall survival (OS) and disease-free survival (DFS) based on gene expression data from The Cancer Genome Atlas (TCGA).

Conclusions
Both the 5hmC signal and fragmentation profiles in 5hmC cfDNA data are sensitive and effective in lung cancer detection and could be incorporated into the diagnostic model to achieve good performance, promoting research focused on clinical diagnostic models based on cfDNA 5hmC data.

Graphical abstract
Computed tomography features and clinical characteristics of gastritis cystica profunda
Authors: Wang Rui , Lu Hao , Yu Juan , Huang Wenpeng , Li Jing , Cheng Ming , Liang Pan , Li Liming , Zhao Huiping , Gao Jianbo 
Published: January 2022

Abstract
Background
The diagnostic evidence of gastritis cystica profunda (GCP) are not adequately described due to its extremely low morbidity. This study aimed to analyze and summarize the comprehensive CT features and clinical characteristics of patients with GCP.

Results
Nineteen patients were enrolled, including eight men and eleven women, with a mean age of 55.53 years. Only one patient had the history of gastric polypectomy. Among the nineteen cases, two cases were in the gastric cardia, four in the gastric fundus, eight in the gastric body and five in the gastric antrum. The shapes were sphere in thirteen patients, hemisphere in five patients and diffuse in one patient. The mean size of eighteen local lesions was 1.63 cm. The cystic changes in submucosa were detected in fifteen patients. Compared with the pancreas, most GCP lesions were hypo-attenuated on unenhanced CT (n = 8), in arterial phase (AP) (n = 17) and venous phase (VP) (n = 11). Fifteen patients had the peak enhancement in VP and two in AP. The rim-like enhancement with central low attenuation was clearly observed in thirteen patients. For the GCP accompanied by adenocarcinoma, the enhancement peak was present in AP and the gradual expansion of enhancement area was in VP. All patients underwent surgical or endoscopic resection. Sixteen cases had remission of symptoms and no recurrence.

Conclusions
The careful analysis of CT features and clinical characteristics can provide support for deepening the understanding of the GCP. However, a more accurate diagnosis depends on histopathological features.
Update of transmission modelling and projections of gambiense human African trypanosomiasis in the Mandoul focus, Chad
Authors: Rock Kat S. , Huang Ching-I , Crump Ronald E. , Bessell Paul R. , Brown Paul E. , Tirados Inaki , Solano Philippe , Antillon Marina , Picado Albert , Mbainda Severin , Darnas Justin , Crowley Emily H. , Torr Steve J. , Peka Mallaye 
Published: January 2022

Abstract
Background
In recent years, a programme of vector control, screening and treatment of gambiense human African trypanosomiasis (gHAT) infections led to a rapid decline in cases in the Mandoul focus of Chad. To represent the biology of transmission between humans and tsetse, we previously developed a mechanistic transmission model, fitted to data between 2000 and 2013 which suggested that transmission was interrupted by 2015. The present study outlines refinements to the model to: (1) Assess whether elimination of transmission has already been achieved despite low-level case reporting; (2) quantify the role of intensified interventions in transmission reduction; and (3) predict the trajectory of gHAT in Mandoul for the next decade under different strategies.

Method
Our previous gHAT transmission model for Mandoul was updated using human case data (2000–2019) and a series of model refinements. These include how diagnostic specificity is incorporated into the model and improvements to the fitting method (increased variance in observed case reporting and how underreporting and improvements to passive screening are captured). A side-by-side comparison of fitting to case data was performed between the models.

Results
We estimated that passive detection rates have increased due to improvements in diagnostic availability in fixed health facilities since 2015, by 2.1-fold for stage 1 detection, and 1.5-fold for stage 2. We find that whilst the diagnostic algorithm for active screening is estimated to be highly specific (95% credible interval (CI) 99.9–100%, Specificity = 99.9%), the high screening and low infection levels mean that some recently reported cases with no parasitological confirmation might be false positives. We also find that the focus-wide tsetse reduction estimated through model fitting (95% CI 96.1–99.6%, Reduction = 99.1%) is comparable to the reduction previously measured by the decline in tsetse catches from monitoring traps. In line with previous results, the model suggests that transmission was interrupted in 2015 due to intensified interventions.

Conclusions
We recommend that additional confirmatory testing is performed in Mandoul to ensure the endgame can be carefully monitored. More specific measurement of cases, would better inform when it is safe to stop active screening and vector control, provided there is a strong passive surveillance system in place.

Graphical Abstract
Supervised machine learning predictive analytics for alumni income
Authors: Gomez-Cravioto Daniela A. , Diaz-Ramos Ramon E. , Hernandez-Gress Neil , Preciado Jose Luis , Ceballos Hector G. 
Published: January 2022

AbstractBackgroundThis paper explores machine learning algorithms and approaches for predicting alum income to obtain insights on the strongest predictors and a ‘high’ earners’ class.MethodsIt examines the alum sample data obtained from a survey from a multicampus Mexican private university. Survey results include 17,898 and 12,275 observations before and after cleaning and pre-processing, respectively. The dataset comprises income values and a large set of independent demographical attributes of former students. We conduct an in-depth analysis to determine whether the accuracy of traditional algorithms can be improved with a data science approach. Furthermore, we present insights on patterns obtained using explainable artificial intelligence techniques.ResultsResults show that the machine learning models outperformed the parametric models of linear and logistic regression, in predicting alum’s current income with statistically significant results (p < 0.05) in three different tasks. Moreover, the later methods were found to be the most accurate in predicting the alum’s first income after graduation.ConclusionWe identified that age, gender, working hours per week, first income and variables related to the alum’s job position and firm contributed to explaining their current income. Findings indicated a gender wage gap, suggesting that further work is needed to enable equality.
Modeling scientometric indicators using a statistical data ontology
Authors: Lopez-Rodriguez Victor , Ceballos Hector G. 
Published: January 2022

AbstractScientometrics is the field of study and evaluation of scientific measures such as the impact of research papers and academic journals. It is an important field because nowadays different rankings use key indicators for university rankings and universities themselves use them as Key Performance Indicators (KPI). The purpose of this work is to propose a semantic modeling of scientometric indicators using the ontology Statistical Data and Metadata Exchange (SDMX). We develop a case study at Tecnologico de Monterrey following the Cross-Industry Standard Process for Data Mining (CRISP-DM) methodology. We evaluate the benefits of storing and querying scientometric indicators using linked data as a mean for providing flexible and quick access knowledge representation that supports indicator discovery, enquiring and composition. The semi-automatic generation and further storage of this linked data in the Neo4j graph database enabled an updatable and quick access model.