bluuebunny/crossref_metadata_2025_split huggingface dataset:
Micro-osteoperforations and Its Effect on the Rate of Tooth Movement: A Systematic Review
Authors: Al-Khalifa Khalifa S. , Baeshen Hosam A. 
Published: July 2020

AbstractProlonged orthodontic treatments have inconvenienced patients and clinicians alike. Surgically assisted techniques for accelerating orthodontic tooth movement have shown promising results in the literature over the years. The minimally invasive nature of micro-osteoperforations (MOPs), however, for enhanced orthodontic tooth movement has recently gained momentum, with many clinical trials conducted on both animals and humans. An electronic search was performed to extract papers using PubMed, Google Scholar, Scopus, and Web of Science. The keywords that were used included “MOP,” “accelerating tooth movement,” “orthodontic tooth movement,” and “regional acceleratory phenomenon.” The studies that met our inclusion criteria were extracted and evaluated in this review. MOPs have been proven time and again, in animal and human studies alike, to increase the rate of orthodontic tooth movement. The application of perforations to cortical bone present in the pathway of teeth, which are specifically to be moved creates transient osteopenia. This reduces the density of the cortical bone, hence speeding up the rate of orthodontic tooth movement. Many techniques have been implemented and perfected to enhance orthodontic tooth movement and shorten the treatment time in the literature. MOPs have proven to be a universally applied, nontechnical, repeatable, and minimally invasive method of accelerating tooth movement, with extremely minimal consequences.
Stem cell lineage survival as a noisy competition for niche access
Authors: Corominas-Murtra Bernat , Scheele Colinda L. G. J. , Kishi Kasumi , Ellenbroek Saskia I. J. , Simons Benjamin D. , van Rheenen Jacco , Hannezo Edouard 
Published: July 2020

Significance
What defines the number and dynamics of the stem cells that generate and renew biological tissues? Although several molecular markers have been described to predict stem cell potential, we propose a complementary approach that mathematically describes “stemness” as an emergent property arising from a stochastic competition for space. We predict from that competition the robust emergence of a region made of functional stem cells, as well as give simple predictions on lineage-survival probability. We test our results with data obtained from intravital live-imaging experiments in mammary gland development, existing data from kidney development, and from the self-renewal of the crypt to show that our framework can predict the number of functional stem cells and lineage-survival probability.
Bioinspired nervous signal transmission system based on two-dimensional laminar nanofluidics: From electronics to ionics
Authors: Teng Yunfei , Liu Pei , Fu Lin , Kong Xiang-Yu , Jiang Lei , Wen Liping 
Published: July 2020

Significance
Mammalian nervous systems, as natural ionic circuitries, have interested researchers with their powerful abilities in environmental perceptions and information transmission, which triggered booming development in artificial prototypes such as biomimetic ionic nanochannels. Most studied artificial ionic systems are more focused on their functions of perception, whereas the ionic information transmission system is rarely reported. Here, two-dimensional laminar nanofluidics are fabricated from MXene nanosheets and the noncontact external electrostatic potential applied patterns to generate and transmit alternating signals, from basic sine to frequency-modulated binary information. This work demonstrates the potentiality of bioinspired nervous signal transmission to simulate the neural ion-carried information system, which might lead to the avenue of alternating current ionics.
TinGa: fast and flexible trajectory inference with Growing Neural Gas
Authors: Todorov Helena , Cannoodt Robrecht , Saelens Wouter , Saeys Yvan 
Published: July 2020

Abstract

Motivation
During the last decade, trajectory inference (TI) methods have emerged as a novel framework to model cell developmental dynamics, most notably in the area of single-cell transcriptomics. At present, more than 70 TI methods have been published, and recent benchmarks showed that even state-of-the-art methods only perform well for certain trajectory types but not others.

Results
In this work, we present TinGa, a new TI model that is fast and flexible, and that is based on Growing Neural Graphs. We performed an extensive comparison of TinGa to five state-of-the-art methods for TI on a set of 250 datasets, including both synthetic as well as real datasets. Overall, TinGa improves the state-of-the-art by producing accurate models (comparable to or an improvement on the state-of-the-art) on the whole spectrum of data complexity, from the simplest linear datasets to the most complex disconnected graphs. In addition, TinGa obtained the fastest execution times, showing that our method is thus one of the most versatile methods up to date.

Availability and implementation
R scripts for running TinGa, comparing it to top existing methods and generating the figures of this article are available at https://github.com/Helena-todd/TinGa.
Individualized multi-omic pathway deviation scores using multiple factor analysis
Authors: Rau Andrea , Manansala Regina , Flister Michael J , Rui Hallgeir , Jaffrézic Florence , Laloë Denis , Auer Paul L 
Published: July 2020

SummaryMalignant progression of normal tissue is typically driven by complex networks of somatic changes, including genetic mutations, copy number aberrations, epigenetic changes, and transcriptional reprogramming. To delineate aberrant multi-omic tumor features that correlate with clinical outcomes, we present a novel pathway-centric tool based on the multiple factor analysis framework called padma. Using a multi-omic consensus representation, padma quantifies and characterizes individualized pathway-specific multi-omic deviations and their underlying drivers, with respect to the sampled population. We demonstrate the utility of padma to correlate patient outcomes with complex genetic, epigenetic, and transcriptomic perturbations in clinically actionable pathways in breast and lung cancer.
The interplay of growth differentiation factor 15 (GDF15) expression and M2 macrophages during prostate carcinogenesis
Authors: Sadasivan Sudha M , Chen Yalei , Gupta Nilesh S , Han Xiaoxia , Bobbitt Kevin R , Chitale Dhananjay A , Williamson Sean R , Rundle Andrew G , Tang Deliang , Rybicki Benjamin A 
Published: July 2020

Abstract
M2 (tumor-supportive) macrophages may upregulate growth differentiation factor 15 (GDF15), which is highly expressed in prostate tumors, but the combined utility of these markers as prognostic biomarkers are unclear. We retrospectively studied 90 prostate cancer cases that underwent radical prostatectomy as their primary treatment and were followed for biochemical recurrence (BCR). These cases also had a benign prostate biopsy at least 1 year or more before their prostate cancer surgery. Using computer algorithms to analyze digitalized immunohistochemically stained slides, GDF15 expression and the presence of M2 macrophages based on the relative density of CD204- and CD68-positive macrophages were measured in prostate: (i) benign biopsy, (ii) cancer and (iii) tumor-adjacent benign (TAB) tissue. Both M2 macrophages (P = 0.0004) and GDF15 (P &lt; 0.0001) showed significant inter-region expression differences. Based on a Cox proportional hazards model, GDF15 expression was not associated with BCR but, in men where GDF15 expression differences between cancer and TAB were highest, the risk of BCR was significantly reduced (hazard ratio = 0.26; 95% confidence interval = 0.09–0.94). In addition, cases with high levels of M2 macrophages in prostate cancer had almost a 5-fold increased risk of BCR (P = 0.01). Expression of GDF15 in prostate TAB was associated with M2 macrophage levels in both prostate cancer and TAB and appeared to moderate M2-macrophage-associated BCR risk. In summary, the relationship of GDF15 expression and CD204-positive M2 macrophage levels is different in a prostate tumor environment compared with an earlier benign biopsy and, collectively, these markers may predict aggressive disease.
Genetic variants in the human leukocyte antigen region and survival of Chinese patients with non-small cell lung carcinoma
Authors: Cheng Lei , Liu Qi , Wang Mengyun , Gu Yanzi , Wang Jialei , Wei Qingyi , Zhang Ruoxin 
Published: July 2020

Abstract
Human leukocyte antigen (HLA) is highly polymorphic, driving antigen presentation, complement cascade and leukocyte maturation against cancer cells. Therefore, we extracted genotyping data in the HLA region from an ongoing Chinese genome-wide association study of non-small cell lung cancer (NSCLC). Using deep sequencing data of 10 689 healthy Han Chinese, we imputed for untyped genetic variants in the HLA region, followed by a two-stage survival analysis of 1531 NSCLC patients. In the discovery stage of 758 patients, we identified 301 out of 15 138 single-nucleotide polymorphisms to be independently associated with overall survival [P &lt; 0.05 and Bayesian false-discovery probability &lt; 0.8]. In further validation of another 773 patients, we confirmed chromosome 6p21, rs241424 (located at intron 3 of TAP2) and rs6457642 as two independent survival predictors. In the combined analysis of 1531 NSCLC patients, rs241424 G&gt;A and rs6457642 C&gt;T were associated with a hazards ratio of 1.26 [95% confidence interval (CI) = 1.14–1.40 and P = 4.04 × 10−6] and 0.76 (95% CI = 0.66–0.87 and P = 1.16 × 10−4), respectively. The analysis of publically available ChIP-sequencing and Hi-C data found that the rs241424 locus was involved in potential cis-regulatory element by a long-range interaction with the HLA-DQA1 promoter. Additional expression quantitative trait loci analysis showed that the rs241424 G&gt;A change decreased HLA-DQA1 mRNA expression. Furthermore, expression levels of HLA-DQA1 were lower in lung cancer tissues than in adjacent normal tissues, and the lower expression was associated with a worse prognosis for patients with lung adenocarcinoma. Collectively, HLA genetic variants may modulate OS of NSCLC patients, possibly via a mechanism of long-range promoter interaction regulating HLA-DQA1 expression.
Targeting cellular senescence in cancer and aging: roles of p53 and its isoforms
Authors: Beck Jessica , Turnquist Casmir , Horikawa Izumi , Harris Curtis 
Published: July 2020

Abstract
Cellular senescence and the associated secretory phenotype (SASP) promote disease in the aged population. Targeting senescent cells by means of removal, modulation of SASP or through cellular reprogramming represents a novel therapeutic avenue for treating cancer- and age-related diseases such as neurodegeneration, pulmonary fibrosis and renal disease. Cellular senescence is partly regulated by the TP53 gene, a critical tumor suppressor gene which encodes 12 or more p53 protein isoforms. This review marks a significant milestone of 40 years of Carcinogenesis publication history and p53 research and 15 years of p53 isoform research. The p53 isoforms are produced through initiation at alternative transcriptional and translational start sites and alternative mRNA splicing. These truncated p53 isoform proteins are endogenously expressed in normal human cells and maintain important functional roles, including modulation of full-length p53-mediated cellular senescence, apoptosis and DNA repair. In this review, we discuss the mechanisms and functions of cellular senescence and SASP in health and disease, the regulation of cellular senescence by p53 isoforms, and the therapeutic potential of targeting cellular senescence to treat cancer- and age-associated diseases.
Clinical Characteristics, Histopathology, and Tissue Immunolocalization of Chikungunya Virus Antigen in Fatal Cases
Authors: Sharp Tyler M , Keating M Kelly , Shieh Wun-Ju , Bhatnagar Julu , Bollweg Brigid C , Levine Rebecca , Blau Dianna M , Torres Jose V , Rivera Aidsa , Perez-Padilla Janice , Munoz-Jordan Jorge , Sanabria Dario , Fischer Marc , Rivera Garcia Brenda , Tomashek Kay M , Zaki Sherif R 
Published: July 2020

Abstract

Background
Death in patients with chikungunya is rare and has been associated with encephalitis, hemorrhage, and septic shock. We describe clinical, histologic, and immunohistochemical findings in individuals who died following chikungunya virus (CHIKV) infection.

Methods
We identified individuals who died in Puerto Rico during 2014 following an acute illness and had CHIKV RNA detected by reverse transcriptase–polymerase chain reaction in a pre- or postmortem blood or tissue specimen. We performed histopathology and immunohistochemistry (IHC) for CHIKV antigen on tissue specimens and collected medical data via record review and family interviews.

Results
Thirty CHIKV-infected fatal cases were identified (0.8/100 000 population). The median age was 61 years (range: 6 days–86 years), and 19 (63%) were male. Death occurred a median of 4 days (range: 1–29) after illness onset. Nearly all (93%) had at least 1 comorbidity, most frequently hypertension, diabetes, or obesity. Nine had severe comorbidities (eg, chronic heart or kidney disease, sickle cell anemia) or coinfection (eg, leptospirosis). Among 24 fatal cases with tissue specimens, 11 (46%) were positive by IHC. CHIKV antigen was most frequently detected in mesenchymal tissues and mononuclear cells including tissue macrophages, blood mononuclear cells, splenic follicular dendritic cells, and Kupffer cells. Common histopathologic findings were intra-alveolar hemorrhage and edema in the lung, chronic or acute tenosynovitis, and increased immunoblasts in the spleen. CHIKV infection likely caused fatal septic shock in 2 patients.

Conclusions
Evaluation of tissue specimens provided insights into the pathogenesis of CHIKV, which may rarely result in septic shock and other severe manifestations.
Direct Evidence of Active SARS-CoV-2 Replication in the Intestine
Authors: Qian Qun , Fan Lifang , Liu Weicheng , Li Jin , Yue Junqiu , Wang Mingwei , Ke Xianliang , Yin Yan , Chen Quanjiao , Jiang Congqing 
Published: July 2020

Abstract

Background
Currently, there is no direct evidence to prove the active replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a patient with clinically confirmed coronavirus disease 2019 (COVID-19) with rectal adenocarcinoma.

Methods
The clinical data were collected during hospitalization and follow-up of this patient. Quantitative reverse transcriptase–polymerasechain reaction (RT-PCR) was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen and immune cell infiltrations.

Results
The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens but not in samples collected 37 days after discharge. Notably, coincident with rectal tissues of surgical specimens testing nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some were SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage.

Conclusions
We first report the direct evidence of active SARS-CoV-2 replication in a patient’s rectum during the incubation period, which might explain SARS-CoV-2 fecal–oral transmission.
Latent Tuberculosis Infection Increases in Kidney Transplantation Recipients Compared With Transplantation Candidates: A Neglected Perspective in Tuberculosis Control
Authors: Shu Chin-Chung , Tsai Meng-Kun , Lin Shu-Wen , Wang Jann-Yuan , Yu Chong-Jen , Lee Chih-Yuan 
Published: July 2020

Abstract

Background
The prevalence and incidence of latent tuberculosis infection (LTBI) in patients with kidney transplantation remain unclear.

Methods
In this prospective study, we enrolled kidney transplantation candidates (KTCs) and recipients (KTRs) from 2014 to 2018. We defined LTBI as a positive result of QuantiFERON-TB Gold In-tube (QFT). We analyzed the predictors for LTBI acquisition and followed up on QFT assay test for 2 years among those initially without LTBI.

Results
Of 425 patients enrolled, 305 (71.8%) patients belonged to the KTC group and 120 (28.2%) to the KTR group. The initial QFT showed positive results in 32 (10.5%) and 24 (20.0%) patients in the KTC and KTR groups, respectively (P = .009). The QFT response value in patients with LTBI was higher in the KTR group than in the KTC group (1.85 vs 1.06 IU/mL, P = .046). Multivariate logistic regression showed that old age, absence of bacillus Calmette–Guérin (BCG) scar, presence of donor-specific antibody, and KTR group were independent factors for positive LTBI. For participants with initial negative QFT, positive QFT conversion within a 2-year follow-up was higher after kidney transplantation (20%) than in KTCs (5.5%) (P = .034).

Conclusions
This study is the first cohort to follow up LTBI status in patients with kidney transplantation and shows its higher prevalence and incidence in KTRs. It indicates that surveillance of LTBI after renal transplantation is important. In addition to status of kidney transplantation, old age, no BCG vaccination, and positive donor-specific antibody are also positive predictors for LTBI.
Non-coding RNAs: update on mechanisms and therapeutic targets from the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart
Authors: Bär Christian , Chatterjee Shambhabi , Falcão Pires Inês , Rodrigues Patrícia , Sluijter Joost P G , Boon Reinier A , Nevado Rosa M , Andrés Vicente , Sansonetti Marida , de Windt Leon , Ciccarelli Michele , Hamdani Nazha , Heymans Stephane , Figuinha Videira Raquel , Tocchetti Carlo G , Giacca Mauro , Zacchigna Serena , Engelhardt Stefan , Dimmeler Stefanie , Madonna Rosalinda , Thum Thomas 
Published: July 2020

Abstract
Vast parts of mammalian genomes are actively transcribed, predominantly giving rise to non-coding RNA (ncRNA) transcripts including microRNAs, long ncRNAs, and circular RNAs among others. Contrary to previous opinions that most of these RNAs are non-functional molecules, they are now recognized as critical regulators of many physiological and pathological processes including those of the cardiovascular system. The discovery of functional ncRNAs has opened up new research avenues aiming at understanding ncRNA-related disease mechanisms as well as exploiting them as novel therapeutics in cardiovascular therapy. In this review, we give an update on the current progress in ncRNA research, particularly focusing on cardiovascular physiological and disease processes, which are under current investigation at the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart. This includes a range of topics such as extracellular vesicle-mediated communication, neurohormonal regulation, inflammation, cardiac remodelling, cardio-oncology as well as cardiac development and regeneration, collectively highlighting the wide-spread involvement and importance of ncRNAs in the cardiovascular system.
International Organization for the Study of Inflammatory Bowel Disease: Global Strategies for Telemedicine and Inflammatory Bowel Diseases
Authors: Lewin Sara , Lees Charles , Regueiro Miguel , Hart Ailsa , Mahadevan Uma 
Published: July 2020

AbstractBefore the onset of the COVID-19 pandemic, the majority of care for inflammatory bowel disease patients was provided in-person. The practice of gastroenterology care has since rapidly transformed, with telemedicine emerging as an essential tool to provide medical care to patients while maintaining social distancing and conserving personal protective equipment. This article provides insight into past and current practices among inflammatory bowel disease specialists and shares regulatory, financial and practical considerations for incorporating telemedicine into clinical practice. Continued government and other payer support for telemedicine and ongoing innovation to provide remote objective patient data will help to sustain the use of telemedicine long after the current pandemic subsides.
Platelet-rich plasma fibrin glue for treatment of chylothorax following cavopulmonary connections
Authors: Tashnizi Mohhamad Abbasi , Maleki Mahmood Hossinzadeh , Javedanfar Omid , Damsaz Mohammadamin , Alamdari Aida Hamidi , Seifalian Alexander M , Asadi Mehdi , Hamidi Alamdari Daryoush 
Published: July 2020

Abstract

OBJECTIVES

The postoperative persistence of chylothorax is a fatal complication of paediatric cardiac surgery. There is an urgent need for an effective treatment of chylothorax. This study reports the application of allogenic platelet-rich plasma fibrin glue (PRP-FG) as a conservative therapy before reoperation.

METHODS
Over a 9-year period, from 2010 to 2019, 27 patients with persistent chylothorax following a cavopulmonary connection, with a mean latency period of 11 days (range 10–15 days), were treated with PRP-FG. These patients were selected because they had not responded positively to initial conservative management plans. The patients were followed up for 9 years.

RESULTS
Twenty-five patients (92%) responded positively to treatment with PRP-FG; 2 patients did not respond to the treatment and died after reoperation. All of the successfully treated patients in follow-up continued to live a healthy life without further complications.

CONCLUSIONS
Recalcitrant chylothorax that persists after paediatric cardiac surgery responded positively to treatment with PRP-FG. This technique precluded the need for another operation and significantly decreased the morbidity and mortality rates.