bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic value of real-time PCR of brain mass lesion in HIV-associated toxoplasmic encephalitis: a case series
Authors: Liang Bo , Yang Si-Yuan , Chen Jia-Min , Liang Ting-Yu , Zhao Hong-Xin , Ding Xing-Huan , Wang Fang , Feng En-Shan 
Published: November 2020

Abstract
Background
Toxoplasmic encephalitis (TE) is a leading cause of brain mass lesions (BML) in human immunodeficiency viruses (HIV)-infected patients. Yet, so far, no accurate diagnostic approach for TE has been developed. Herein, we presented a case series (9 HIV-infected patients with TG confirmed by RT-PCR of BML) to assess the diagnostic value of reverse transcription-polymerase chain reaction (RT-PCR) on TE.

Methods
A total of 9 HIV-infected patients with TE confirmed by RT-PCR of BML were included in this study. Clinical data, including clinical symptoms, blood and CSF analysis, neuroimaging features, histopathological characteristics, treatment, and prognosis, were assessed in all patients. According to the results of RT-PCR of BML, all the patients received oral administration of trimethoprim-sulfamethoxazole combined with antiretroviral therapy (ART). Patients were followed up by telephone or outpatient service.

Results
There were 8 male and 1 female patients; their age ranged from 26 to 56 years-old. The main symptom was intracranial hypertension (6/9). Six patients presented multiple brain lesions, which were mainly located in the supratentorial area (7/9). CD4+ count ranged from 11 to 159 cells/μl (median 92 cells/μl), and serological HIV viral load 0–989190 copies/ml (median 192836 copies/ml). IgG and IgM against serum TG were positive in 7 and 1 patients, respectively. Moreover, regarding CSF, IgG against TG was positive in 3 patients, while all patients were negative for IgM. The neuroimaging features on MRI showed no specificity. Four patients were diagnosed with TE by histopathological findings. After receiving anti-Toxoplasma therapy, 8 (8/9) patients improved clinically to a considerable extent.

Conclusions
The application of RT-PCR of BML, together with conventional methods, may significantly improve the diagnostic efficiency of TE.

Graphical Abstract
Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis
Authors: Wang Wen-Jun , Li Ling-Yu , Cui Jiu-Wei 
Published: November 2020

Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
Gene expression identifies patients who develop inflammatory arthritis in a clinically suspect arthralgia cohort
Authors: Niemantsverdriet Ellis , van den Akker Erik B. , Boeters Debbie M. , van den Eeden Susan J. F. , Geluk Annemieke , van der Helm-van Mil Annette H. M. 
Published: November 2020

AbstractBackgroundEstablished rheumatoid arthritis (RA) patients display differentially expressed genes coding for cytokine/chemokine-mediated immunity compared to healthy controls. It is unclear, however, if in the pre-arthritis phase of clinically suspect arthralgia (CSA) expression of immune genes differ between patients who do or do not develop clinically evident inflammatory arthritis (IA).MethodsTwo hundred thirty-six consecutive patients presenting with arthralgia clinically suspected for progression to RA were followed until IA development or else for median 24 months (IQR 12–26). Baseline whole blood RNA expression was determined for a previously identified set of 133 genes associated with the innate and adaptive immune system by dual-color reverse-transcription multiplex ligation-dependent probe amplification (dcRT-MLPA) profiling. Cox proportional hazard models were used.ResultsTwenty percent of CSA patients developed IA. After correction for multiple testing, expression levels of six genes (IFNG, PHEX, IGF-1, IL-7R, CD19, CCR7) at the time of presentation were associated with progression to IA. PHEX and IGF-1 were highly correlated with each other (ρ = 0.97). In multivariable analysis correcting for the different genes, expressions of IL-7R and IGF-1 were independently associated with IA development (p = 0.025,p = 0.046, respectively). Moreover, IL-7R and IGF-1 remained significantly associated even after correction for known predictors (ACPA, CRP, imaging-detected subclinical joint inflammation;p = 0.039,p = 0.005, respectively). These genes are also associated with RA development.ConclusionsIL-7R and IGF-1 were differentially expressed between CSA patients who did or did not progress to IA, independent from regularly used predictors. These biomarkers may become helpful in prognostication of CSA patients. Furthermore, because both genes are associated with T cell functioning, T cell dysregulation may mediate progression from arthralgia to arthritis.
Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells
Authors: Zhao Xin , Gao Shouguo , Kajigaya Sachiko , Liu Qingguo , Wu Zhijie , Feng Xingmin , Zhang Fengkui , Young Neal S. 
Published: November 2020

Abstract

Objective
Single cell methodology enables detection and quantification of transcriptional changes and unravelling dynamic aspects of the transcriptional heterogeneity not accessible using bulk sequencing approaches. We have applied single-cell RNA-sequencing (scRNA-seq) to fresh human bone marrow CD34+ cells and profiled 391 single hematopoietic stem/progenitor cells (HSPCs) from healthy donors to characterize lineage- and stage-specific transcription during hematopoiesis.

Results
Cells clustered into six distinct groups, which could be assigned to known HSPC subpopulations based on lineage specific genes. Reconstruction of differentiation trajectories in single cells revealed four committed lineages derived from HSCs, as well as dynamic expression changes underlying cell fate during early erythroid-megakaryocytic, lymphoid, and granulocyte-monocyte differentiation. A similar non-hierarchical pattern of hematopoiesis could be derived from analysis of published single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), consistent with a sequential relationship between chromatin dynamics and regulation of gene expression during lineage commitment (first, altered chromatin conformation, then mRNA transcription). Computationally, we have reconstructed molecular trajectories connecting HSCs directly to four hematopoietic lineages. Integration of long noncoding RNA (lncRNA) expression from the same cells demonstrated mRNA transcriptome, lncRNA, and the epigenome were highly homologous in their pattern of gene activation and suppression during hematopoietic cell differentiation.
Using pollen DNA metabarcoding to profile nectar sources of urban beekeeping in Kōtō-ku, Tokyo
Authors: Tanaka Keisuke , Nozaki Akinobu , Nakadai Hazuki , Shiwa Yuh , Shimizu-Kadota Mariko 
Published: November 2020

AbstractObjectiveApis melliferais a species of honeybee that has been introduced around the world as an industrial beekeeping species. Recently, urban beekeeping has attracted attention as a means of ecosystem protection and urban greening. This study aimed to investigate nectar sources of urban beekeeping in Kōtō-ku, Tokyo using pollen DNA metabarcoding.ResultsWe extracted DNA from pollen collected by the honeybees of a local urban beekeeping operation. DNA metabarcoding analysis was carried out by sequencing a part of therbcL region of the chloroplast genome. A total of 31 samples collected between mid-March, 2018 and mid-October, 2018 yielded 54 operational taxonomic units (OTUs) comprising 14 families, 32 genera, and 8 species. Whereas 5 OTUs were profiled throughout all seasons, 38 OTUs were season-specific (spring, summer, or autumn). Therefore, we were able to infer seasonal nectar sources for the beekeeping operation at the family or genus level, as well as at the species level to a lesser extent. Our pollen-sampling strategy was effective for profiling season-specific nectar sources, with the exception of a few anomalies that can be accounted for by out-of-season flowering associated with artificial gardening and/or pollen accumulation over multiple seasons.
The effect of climatic and geographical factors on breast cancer in Iran
Authors: Maryanaji Zohreh 
Published: November 2020

Abstract
Objective
By studying the effect of environmental factors on health, it is clear that geographical, climatic and environmental factors have a significant impact on human health. This study, based on the data of the patients with breast cancer in Iran since 2010 to 2014 and using the statistical methods has determined the effect of geographical features of Iran (solar radiation status, radiation angle) on the frequency and distribution of this disease.

Results
The maximum amount of total solar radiation occurs in the vicinity (surrounding) of the tropic of cancer, which covers some parts of the south of Iran and in the atmosphere of the northern latitudes of Iran. The amount of humidity and cloudiness is more than the southern latitudes, which causes more reflection of short waves of the sun during the day. Findings showed that the rate of breast cancer in low latitudes is higher than high latitudes. It was also found that with increasing longitude, the rate of cancer increases significantly due to the high thickness of the atmosphere and receiving more sunlight in the electromagnetic spectrum, as well as dry air and low water vapor in low altitude areas of eastern and southeastern Iran.
First report on molecular basis of potato leaf roll virus (PLRV) aggravation by combined effect of tuber and prevailing aphid
Authors: Kumar Ravi Ranjan , Ansar Mohammad , Rajani Kumari , Kumar Jitesh , Ranjan Tushar 
Published: November 2020

Abstract

Objective
The Potato Leaf Roll Virus (PLRV) is one of the most devastating virus causing severe yield losses worldwide in potato. The comprehensive observations were made to study the PLRV infestation in major potato growing areas of Bihar (India) and further detailed molecular basis of PLRV aggravation was established.

Results
Although aphids population were found comparatively lower with maximum symptomatic plants, our molecular data further confirms the presence of PLRV in all possible symptomatic tissues such as tubers, shoots and leaves. For the first time, we have proposed molecular basis of aggravation of PLRV, where tuber acts as a reservoir during off-season and further transmitted by aphids.
Toward the identification of a phytocannabinoid-like compound in the flowers of a South African medicinal plant (Leonotis leonurus)
Authors: Hunter E. , Stander M. , Kossmann J. , Chakraborty S. , Prince S. , Peters S. , Loedolff Bianke 
Published: November 2020

Abstract

Objective
Current global trends on natural therapeutics suggest an increasing market interest toward the use and discovery of new plant-derived therapeutic compounds, often referred to as traditional medicine (TM). The Cannabis industry is currently one such focal area receiving attention, owing to the occurrence of phytocannabinoids (pCBs) which have shown promise in health-promotion and disease prevention. However, the occurrence of pCBs in other plant species are often overlooked and rarely studied. Leonotis leonurus (L.) R. Br. is endemic to South Africa with a rich history of use in TM practices amongst indigenous people and, has been recorded to induce mild psychoactive effects akin to Cannabis. While the leaves have been well-reported to contain therapeutic phytochemicals, little information exists on the flowers. Consequently, as part of a larger research venture, we targeted the flowers of L. leonurus for the identification of potential pCB or pCB-like compounds.

Results
Flower extracts were separated and analyzed using high performance thin layer chromatography (HPTLC). A single pCB candidate was isolated from HPTLC plates and, using liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS), we could successfully group this compound as a fatty amide and tentatively identified as 7,10,13,16-Docosatetraenoylethanolamine (adrenoyl-EA), a known bioactive compound.
Red flags for the differential diagnosis of granulomatous mastitis: a case report
Authors: Chalmers Richard , McClellan Patrick , Silva Vixey , Shutt Natalie , Restini Carolina 
Published: November 2020

Abstract

Background
Granulomatous mastitis (GM) is a rare benign chronic inflammatory breast disease. GM presents as a heterogeneous illness with variable clinical presentations, and its diagnosis is usually made by exclusion. There are no guidelines for the treatment of GM. This manuscript describes the management of a patient with GM, initially unsuccessfully treated outside our clinic under a diagnosis of mastitis. The patient’s history, physical examination, and needle biopsy flagged the patient’s findings as nonmalignant; however, imaging studies indicated a tumor. Differential diagnosis became a critical element of her care. This case report represents a valuable resource to foster more assertive clinical practice in managing patients with GM. The case coordination and its course were led by a team from an outreach clinic that provides health care services to underserved communities in the state of Michigan.

Case presentation
A 41-year-old G1P1 Hispanic female immigrant from Central America presented with a rare breast disease, granulomatous mastitis. A similar presentation occurred 5 years before pregnancy when she had an episode of pain and swelling in the left breast, which resolved spontaneously. She sought our services after being diagnosed with mastitis that was unsuccessfully treated. Physical examination revealed a nodular mass in the outer quadrants of the left breast without regional lymphadenopathy. Needle biopsy showed fibrohistiocytic and florid inflammatory reactions, with no evidence of invasive carcinoma. However, this result was inconsistent with the degree of abnormality revealed by the mammogram (BI-RADS grade 5), ultrasound, and physical examination. Full incisional biopsy revealed cystic neutrophilic GM. The surgical procedure, antibiotics, and corticosteroids resulted in a successful combination to secure the stable control of the symptoms and progression of this rare benign breast disease to date.

Conclusions
This patient’s case highlights the importance of integrated communication among front-line primary care and other health care professionals to reduce the risk of invasive procedures and avoid institutional costs. GM is a rare disease. We raised the manifold red flags in which the multiple professional chains recruited to care for this patient were concerning for advanced breast cancer. The lack of experience and evidence-based medicine contributed to the contradictory interpretation of the findings on GM's diagnosis.
Autologous adipose-derived stem cells for the treatment of complex cryptoglandular perianal fistula: a prospective case-control study
Authors: Zhang Yang , Ni Min , Zhou Chungen , Wang Yehuang , Wang Yaxian , Shi Yang , Jin Jing , Zhang Rui , Jiang Bin 
Published: November 2020

Abstract

Background
Complex cryptoglandular perianal fistula (CPAF) is a kind of anal fistula that may cause anal incontinence after surgery. Minimally invasive surgery of anal fistula is constantly emerging. Over the past 20 years, there are several sphincter-sparing surgeries, one of which is autologous adipose-derived stem cell (ADSC) transplantation. However, to date, there is no study regarding the treatment of complex CPAF with ADSC in China. This is the first study in China on the treatment of complex CPAF with ADSC to evaluate its safety and efficacy.

Methods
Totally, 24 patients with complex CPAF were enrolled in this prospective case-control study from January 2018 to December 2019 in the National Colorectal Disease Center of Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine. Patients were divided into ADSC group and endorectal advancement flap (ERAF) group according to their desire. The healing of fistulas (healing of all treated fistulas at baseline, confirmed by doctor’s clinical assessment and magnetic resonance imaging or transrectal ultrasonography) was evaluated at week 12 after treatment. In addition to their safety evaluation based on adverse events monitored at each follow-up, the patients were also asked to complete some scoring scales at each follow-up including pain score with visual analog score (VAS) and anal incontinence score with Wexner score.

Results
The closure rates within ADSC group and ERAF group at week 12 were 54.55% (6/11) and 53.85% (7/13), respectively, without significant difference between them. VAS score in ADSC group was significantly lower than that in ERAF group at the 5th day postoperatively [1(0,2) VS 2(2,4), p = 0.011], but no differences were observed at the other time. Wexner score of all patients was not increased with no significant differences between the two groups. Adverse events were observed fewer in ADSC group (27.27%) than that in ERAF group (53.85%), but there was no significant difference between them.

Conclusion
This study indicated safety and efficiency of ADSC for the treatment of complex CPAF in the short term, which is not inferior to that of ERAF. ADSC may provide a promised and potential treatment for complex CPAF conforming to the future of the treatment, which is reconstruction and regeneration.

Trail registration
ChiCTR, ChiCTR1800014599. Registered 23 January 2018—retrospectively registered, http://www.chictr.org.cn/showproj.aspx?proj=24548
Memory-assisted reinforcement learning for diverse molecular de novo design
Authors: Blaschke Thomas , Engkvist Ola , Bajorath Jürgen , Chen Hongming 
Published: November 2020

Abstract
In de novo molecular design, recurrent neural networks (RNN) have been shown to be effective methods for sampling and generating novel chemical structures. Using a technique called reinforcement learning (RL), an RNN can be tuned to target a particular section of chemical space with optimized desirable properties using a scoring function. However, ligands generated by current RL methods so far tend to have relatively low diversity, and sometimes even result in duplicate structures when optimizing towards desired properties. Here, we propose a new method to address the low diversity issue in RL for molecular design. Memory-assisted RL is an extension of the known RL, with the introduction of a so-called memory unit. As proof of concept, we applied our method to generate structures with a desired AlogP value. In a second case study, we applied our method to design ligands for the dopamine type 2 receptor and the 5-hydroxytryptamine type 1A receptor. For both receptors, a machine learning model was developed to predict whether generated molecules were active or not for the receptor. In both case studies, it was found that memory-assisted RL led to the generation of more compounds predicted to be active having higher chemical diversity, thus achieving better coverage of chemical space of known ligands compared to established RL methods.
New general decay result for a system of two singular nonlocal viscoelastic equations with general source terms and a wide class of relaxation functions
Authors: Al-Gharabli Mohammad M. , Al-Mahdi Adel M. , Messaoudi Salim A. 
Published: November 2020

Abstract
This work is concerned with a system of two singular viscoelastic equations with general source terms and nonlocal boundary conditions. We discuss the stabilization of this system under a very general assumption on the behavior of the relaxation function $k_{i}$

k
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, namely, $$\begin{aligned} k_{i}^{\prime }(t)\le -\xi _{i}(t) \Psi _{i} \bigl(k_{i}(t)\bigr),\quad i=1,2. \end{aligned}$$

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(
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,

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1
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.
We establish a new general decay result that improves most of the existing results in the literature related to this system. Our result allows for a wider class of relaxation functions, from which we can recover the exponential and polynomial rates when $k_{i}(s) = s^{p}$

k
i

(
s
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=

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p

and p covers the full admissible range $[1, 2)$
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.
Dynamics of the rumor-spreading model with hesitation mechanism in heterogenous networks and bilingual environment
Authors: Yang Shuai , Jiang Haijun , Hu Cheng , Yu Juan , Li Jiarong 
Published: November 2020

AbstractIn this paper, a novel rumor-spreading model is proposed under bilingual environment and heterogenous networks, which considers that exposures may be converted to spreaders or stiflers at a set rate. Firstly, the nonnegativity and boundedness of the solution for rumor-spreading model are proved by reductio ad absurdum. Secondly, both the basic reproduction number and the stability of the rumor-free equilibrium are systematically discussed. Whereafter, the global stability of rumor-prevailing equilibrium is explored by utilizing Lyapunov method and LaSalle’s invariance principle. Finally, the sensitivity analysis and the numerical simulation are respectively presented to analyze the impact of model parameters and illustrate the validity of theoretical results.
Constructions of the soliton solutions to the good Boussinesq equation
Authors: Almatrafi Mohammed Bakheet , Alharbi Abdulghani Ragaa , Tunç Cemil 
Published: November 2020

AbstractThe principal objective of the present paper is to manifest the exact traveling wave and numerical solutions of the good Boussinesq (GB) equation by employing He’s semiinverse process and moving mesh approaches. We present the achieved exact results in the form of hyperbolic trigonometric functions. We test the stability of the exact results. We discretize the GB equation using the finite-difference method. We also investigate the accuracy and stability of the used numerical scheme. We sketch some 2D and 3D surfaces for some recorded results. We theoretically and graphically report numerical comparisons with exact traveling wave solutions. We measure the$L_{2}$L2 error to show the accuracy of the used numerical technique. We can conclude that the novel techniques deliver improved solution stability and accuracy. They are reliable and effective in extracting some new soliton solutions for some nonlinear partial differential equations (NLPDEs).