bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of an extremely patient-friendly progestin-primed ovarian stimulation protocol in normal and high responders by comparing with conventional antagonist protocol: a retrospective study
Authors: Huang Chen-Yu , Chen Guan-Yeu , Shieh Miawh-Lirng , Li Hsin-Yang 
Published: April 2020

Abstract
Background. Our previous study has shown a satisfactory reproductive outcome resulting from the extremely patient-friendly ovarian stimulation protocol of long-acting follicle stimulation hormone (FSH) plus oral medroxyprogesterone acetate (MPA). The present study was aimed to compare the efficacy of the extremely patient-friendly ovarian stimulation protocol with that of antagonist protocol.Methods. A retrospective study was conducted on normal and high responders aged from 24 to 39 years starting ovarian stimulation for IVF/ICSI with long-acting FSH at early follicular phase in a tertiary fertility center in Taiwan between December 2016 and August 2017. To prevent premature luteinizing hormone (LH) surge, oral MPA was applied in some cycles (group 1), whereas antagonist protocol was applied in other cycles (group 2). Freezing all embryos was applied to all patients in both groups. Duration of stimulation, number of shots and visits before trigger, incidence of premature LH surge, number of oocytes retrieved, fertilization rate, cleavage rate, rate of good embryos available, incidence of ovarian hyperstimulation syndrome, cumulative clinical pregnancy rate, and cumulative live birth rate per retrieval were compared between groups. Results. One hundred and ten cycles of IVF/ICSI were included, among which there were fifty-seven cycles in group 1 and fifty-three cycles in group 2. Starting with long-acting FSH, group 1 (MPA) required much fewer injections and visits but had comparable reproductive outcomes to those in group 2 (antagonist protocol).Conclusions. Long-acting FSH plus MPA use for ovarian stimulation is extremely friendly for the patients and demonstrates satisfactory stimulation and reproductive outcomes that are comparable to those of antagonist protocol.
miR-4668-5p is up-regulated in serum of patients with pancreatic cancer
Authors: Lv Pengfei , Hao Zhengwen , Zhang Haoruo , Li Jun 
Published: April 2020

Abstract
Backgroud:

Pancreatic cancer is the most common of gastrointestinal tumor, with a high malignancy and poor prognosis,and early and effective diagnosis is the key for prolonging patient’s overall survival, especially for fluid biopsy.
Methods

In this study, expression profile array was downloaded from GEO database, and differentially expressed miRNAs in serum were screened from patients with pancreatic cancer and healthy individuals, then co-expressed serum miRNAs in pancreatic cacner patients was analyzed by R software with weighted correlation network analysis(WGCNA) package. Finally, key differentially expressed miRNA was verified in serum of 16 patients with pancreatic cancer and 10 healthy individuals by quantitative real-time PCR (qRT-PCR).
Results

Results found that there were eleven differentially expressed miRNAs(miR-155-5p, miR-4668-5p, miR-3613-3p, -miR-3201, miR-548ac, miR-486-5p, miR-548a-3p, miR-8084, miR-455-3p, miR-6068, and miR-1246) between pancreatic cancer and healthy individuals. WGCNA results further found that miR-4668-5p has a higher associated modules compared to other differentially expressed miRNAs. Then, the expression level of miR-4668-5p was further verified, and results found that serum miR-4668-5p expression level was significantly higher in patients with pancreatic cancer than that of healthy individuals.
Conclusion

Our results firstly substantiated that miR-4668-5p was significantly up-regulated in serum of patients with pancreatic cancer, which may be a potential biomarker for pancreatic cancer diagnosis.
Detailed comparison of the da Vinci Xi and S surgical systems for transaxillary thyroidectomy
Authors: Yu Da Young , Lee Hye Yoon , Kim Woo Young , Kim Hoon Yub , Lee Jae Bok , Son Gil Soo , Chang Young Woo 
Published: April 2020

Abstract
Background
Robotic surgical systems have evolved over time. The da Vinci Xi system was developed in 2014 and was expected to solve the shortcomings of the previous S system. Therefore, we conducted this study to compare these two systems and identify if the Xi system truly improves surgical outcomes.
Methods
In this retrospective study, a total of 86 patients with unilateral papillary thyroid carcinoma without central lymph node involvement underwent gasless transaxillary hemithyroidectomy using two robotic systems, the da Vinci S and Xi. Forty patients were in the da Vinci S group and 46 patients were in the da Vinci Xi group. All surgeries were performed by one surgeon (YWC). All surgery video files were analyzed to compare the duration of each surgical step.
Results
The total operation time was significantly shorter in the Xi group than in the S group (153.0 min vs. 105.7 min, p < 0.01). Time for robot docking was shorter in the Xi group (19.8 min vs. 10.6 min, p < 0.01), and all procedures performed in the console also required a shorter time in this group. The overall complication rate did not differ significantly (p = 0.464).
Conclusions
The da Vinci Xi system made robotic thyroidectomy easier and faster without increasing the complication rate. It is a safe and valuable system for robotic thyroidectomy.
Effect of Self-Compassion Intervention Based on a Religious Perspective on the Anxiety and Quality of Life of Infertile Women: A quasi-experimental study
Authors: Rezapour-Mirsaleh Yasser , Abolhasani Fatemeh , Amini Raziyeh , Choobforoushzadeh Azadeh , Masoumi Sepideh , Shameli Leila 
Published: April 2020

Abstract
Background Anxiety is one of the common psychological problems among infertile women, which affects their quality of life. The purpose of this study was to determine the effect of self-compassion intervention based on religious perspective on the anxiety and quality of life of infertile women. Methods A qusai-experimental design with experimental and control groups was used. 24 women who lived in Maybod city, Iran, and were referred to Yazd reproductive sciences institute selected by available sampling and randomly assigned to experimental and control groups. The participants of experimental group received 8 sessions self-compassion focused intervention based on religious instructions and control group was put on the waiting list. Data were collected using Quality of Life Questionnaire in Infertile Couples Questionnaire (QOLICQ) and Beck anxiety inventory (BDI) in pretest and posttest phase and then analyzed using multivariate analysis covariance (MANCOVA). Results The results showed as compared to control group at the post-test phase, the quality of life (p< .001) and anxiety (p< .001) of infertile women increased and decreased, respectively, in the experimental group. Conclusion Infertility medical centers can use self-compassion intervention based on a religious approach as a complementary psychological intervention, alongside with medical interventions, to improve the quality of life and reduce anxiety in infertile women.
Eckol alleviates intestinal dysfunction during suckling-to-weaning transition via modulation of PDX1 and HBEGF
Authors: Lee Sang In , Kim In Ho 
Published: April 2020

Abstract
Background
Maintaining intestinal health in livestock is critical during weaning. Although intestinal dysfunction during this period can be alleviated by phlorotannins including eckol, the precise mechanisms are not fully understood. We addressed this question by evaluating changes in gene expression and intestinal function after treatment with eckol during the suckling-to-weaning transition. The biological roles of differentially expressed genes in intestinal development were investigated by assessing intestinal wound healing and barrier function and associated signaling pathways, along with oxidative stress levels.
Results
We identified 890 differentially expressed genes in the intestine whose expression was altered by eckol treatment including pancreatic and duodenal homeobox (PDX)1, which directly regulate the expression of heparin-binding epidermal growth factor-like growth factor (HBEGF) to preserve intestinal barrier function and promote wound healing via phosphoinositide 3-kinase (PI3K)/AKT and P38 signaling. Additionally, eckol alleviated H2O2-induced oxidative stress via PI3K/AKT, P38, and 5' AMP-activated protein kinase signaling, improved growth, and reduced oxidative stress and intestinal permeability in pigs during weaning.
Conclusions
Eckol modulates intestinal barrier function, wound healing, and oxidative stress via PDX/HBEGF and improves growth during the suckling-to-weaning transition, suggesting that it can be used as a feed supplement to preserve intestinal function during this process in pigs and other livestock.
Endometrial neuroendocrine carcinoma frequently associated with mismatch repair deficiency
Authors: Zhou Feng , Xu Mengfei , Chen Qin , Zhang Xiaofei , Chen Hao , Zheng Wenxin 
Published: April 2020

Abstract
Background: Endometrial neuroendocrine carcinoma (NEC) is a uncommon histologic subtype of endometrial cancer. It is currently unclear if the endometrial NEC has any particular relationship with mismatch repair (MMR) protein expression patterns. Here we report 3 endometrial NEC cases showing loss of MMR expression.Case presentation: The cancers had two components with one poorly differentiated or NEC component, accounting for 60–90% of the neoplasms and the other of well differentiated glandular component. The NEC cells mainly showed solid sheets and organoid patterns, whereas insular, trabecular and rosette/pseudorosette patterns were also found. The NEC component was composed of cells with large, polygonal, vesicular nuclei, prominent nucleoli, and abundant eosinophilic cytoplasm. In all cases, the NEC component was diffusely positive for p16 and at least 2 of the 3 neuroendocrine markers (CGA, SYN, CD56) reactive in > 10% of the cancer cells. Loss of MMR protein expression was found in all three cases with loss of MLH1 in cases 1 and 2 and loss of MSH2 and MSH 6 in case 3. No PMS2 loss was found. In addition, aberrant TP53 and SMARCB1 (INI1) expression was found in case 3 only. All patients underwent total abdominal hysterectomy and bilateral salpingo-oophorectomy, and two of them received postoperative chemotherapy and/or radiation therapy. The patients remained alive with no disease for 51, 17 and 6 months, respectively.Conclusion: Endometrial NEC is frequently associated with MMR deficiency, some of which may have a better prognosis than we expect.
New sight: rapid monitor of intracellular water information in plant leaves based on electrophysiological parameters
Authors: Zhang C. , Wu Yanyou , Su Y. , Xing D.K. , Dai Y. , Wu Y.S. , Fang L. 
Published: April 2020

Abstract
Background: Intracellular water in plant leaves is paramount importance to physiological and biochemical processes. Water changes trigger the rapid response of plant electrophysiological information. In this study, plant electrophysiological information was firstly used to rapid monitor intracellular water information in plant leaves. Results: Based on the thermodynamics laws, the fitting equations between plant electrophysiological parameters and clamping force were innovative established. Subsequently, leaf intrinsic electrophysiological parameters, intracellular water-holding capacity (IWHC), water use efficiency (IWUE), water-holding time (IWHT) and water transfer rate (WTR), were firstly developed and applied. The results show that the leaves of Broussonetia papyrifera in the cultivated soil had higher IWHC, WTR and water content than in the moderate rocky desertification soil. The leaf IWHC, WTR and water content of the herbaceous plants were higher than that of the woody plants. Solanum tuberosum had higher leaf IWHC, WTR and lower IWUE, IWHT, as compared to Capsicum annuum. Conclusions: These indexes strongly reveal the life phenomenon of the intracellular water metabolism in plant leaves. This study highlights that the online electrophysiological parameters promise a new sight for intracellular water metabolism in plants.
Decoding the structure of RNA-dependent RNA-polymerase (RdRp), understanding the ancestral relationship and dispersion pattern of 2019 Wuhan Coronavirus
Authors: Khan Abbas , Khan Mazhar , Saleem Shoaib , Babar Zainib , Ali Arif , Khan Abdul Aziz , Sardar Zain , Hamayun Fahad , Ali Syed Shujait , Wei Dong-Qing 
Published: April 2020

Abstract
Most recently, an outbreak of severe pneumonia caused by the infection of 2019-nCoV, a novel coronavirus first identified in Wuhan, China, imposes serious threats to public health. Upon infecting host cells, coronaviruses assemble a multi-subunit RNA-synthesis complex of viral non-structural proteins (nsp) responsible for the replication and transcription of the viral genome. Therefore, the role and inhibition of nsp12 are indispensable. Since there is no crystallographic structure of RdRp is available, so, here, we present the 3-dimensional structure of the 2019-nCoV nsp12 polymerase using a computational approach. nsp12 of 2019-nCoV possesses an architecture common to all viral polymerases as well as a large N-terminal extension. This structure illuminates the assembly of the coronavirus core RNA-synthesis machinery, provides key insights into nsp12 polymerase catalysis and fidelity, and acts as a template for the design of novel antiviral therapeutics. Besides, the experimental structure could reveal the organization in a more sophisticated way. Furthermore, the ancestral state reconstruction suggests the possible evolution of nCoV in Wuhan China and its dispersal to the USA. The result of our analyses postulates the possible dispersal of nCoV from the USA and Shenzhen back to Wuhan. This disclosing of valuable knowledge regarding the 3D structure of 2019-nCoV nsp12 architecture, ancestral relation, and dispersion pattern could help to design effective therapeutic candidates against the coronaviruses and design robust preventive measurements.
Heavy metal pollution status in surface sediments of the Khajeh Kory River, north Iran
Authors: Zare Khosheghbal Maryam , Esmaeilzadeh Marjan , Ghazban Fereydoun , Charmsazi Mohammad Ebrahim 
Published: April 2020

Abstract
This study aimed at exploring the extent of likely sources of heavy metal pollution in sediments of the Khajeh Kory riverbed in the north of Iran. In order to assess the heavy metal contamination, samples from surface sediments in 10 stations covering the river were collected and analysed to determine heavy metal contents including Cd, Cu, Ni, Pb, Zn, Mn, Co, Al, and Fe. Three guidelines were applied to assess the heavy metal contamination. Compared with the global average values, the calculated enrichment factors indicated high values for Fe, Mn, Cd, Co, and Cu, and very high values for Pb and Zn. The results obtained from principal component analysis revealed that the geogenic and anthropogenic sources were the main causes of the widespread enrichment of heavy metals in the riverbed sediments. The results suggested that the riverbed sediments were contaminated with heavy metals, which contribute to the freshwater toxicity in the ecosystem of the Khajeh Kory River.
Visible-light-driven photocatalytic degradation of rhodamine B in water by BiOClxI1−x solid solutions
Authors: Xu Huan-Yan , Lu Dan , Tan Qu , He Xiu-Lan , Qi Shu-Yan 
Published: April 2020

AbstractBismuth oxyhalides (BiOXs, X = Cl, Br and I) are emerging photocatalytic materials with unique layered structure, flexible band structure and superior photocatalytic activity. The purpose of this study was to develop a facile alcoholysis route to prepare BiOClxI1−x nanosheet solid solutions at room temperature. X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), UV-vis diffuse reflectance spectroscopy (UV-vis DRS), photoluminescence emission spectroscopy (PL) and Brunauer–Emmett–Teller (BET) surface area analyzer were used to characterize the as-prepared photocatalysts. These results revealed that two-dimension BiOClxI1−x nanosheet solid solutions could be obtained with high percentage of {001} crystal facets exposed. Moreover, the formation of solid solution could regularly change the optical absorption thresholds and band gaps of BiOClxI1−x photocatalysts. The photocatalytic experiments indicated that BiOCl0.75I0.25 exhibited the highest photocatalytic performance for the degradation of Rhodamine B (RhB) under simulated sunlight irradiation and the photocatalytic process followed a pseudo-first-order kinetic equation. A possible mechanism of RhB photodegradation over BiOClxI1−x solid solutions was proposed based on the structural properties of BiOClxI1−x solid solutions and RhB photosensitization.
Across the “Sweetest” Properties of Human Breast Milk: Focus on Oligosaccharides
Authors: Bardanzellu Flaminia , Reali Alessandra , Marcialis Maria A. , Fanos Vassilios 
Published: April 2020

Introduction:
Breast Milk (BM), containing nutrients and bioactive components, represents
the best source for neonatal nutrition and determines short- and long- term benefits. Human
milk oligosaccharides (HMOs) play an active role in these pathophysiological mechanisms. In fact,
they influence the shaping of breastfed infant’s gut microbiota, promote intestinal development,
confer protection against intestinal or systemic infections modulating immune system; moreover,
HMOs determine extra-intestinal effects on several target organs, i.e reducing necrotizing enterocolitis
rate or improving brain development.

Aims:
In this review, we analyze the great inter- and intra-individual variability of BM HMOs, investigating
maternal, genetic and environmental factors modulating their composition. Moreover,
we provide an update regarding HMOs’ unique properties, underlining their complex interaction
with intestinal microbiota and host-derived metabolites. The possible HMOs’ influence on extraintestinal
bacterial communities, potentially influencing newborns’ and even lactating mothers’
health, have been hypothesized. Finally, recognized HMOs’ crucial role, we underline the promising
opportunities showed by their addition in formula milk, to make it more similar to maternal
milk itself.
A Review on the Methods of Peptide-MHC Binding Prediction
Authors: Liu Yang , Ouyang Xia-hui , Xiao Zhi-Xiong , Zhang Le , Cao Yang 
Published: April 2020

Background:
T lymphocyte achieves an immune response by recognizing antigen
peptides (also known as T cell epitopes) through major histocompatibility complex (MHC)
molecules. The immunogenicity of T cell epitopes depends on their source and stability in
combination with MHC molecules. The binding of the peptide to MHC is the most selective step,
so predicting the binding affinity of the peptide to MHC is the principal step in predicting T cell
epitopes. The identification of epitopes is of great significance in the research of vaccine design
and T cell immune response.

Objective:
The traditional method for identifying epitopes is to synthesize and test the binding
activity of peptide by experimental methods, which is not only time-consuming, but also
expensive. In silico methods for predicting peptide-MHC binding emerge to pre-select candidate
peptides for experimental testing, which greatly saves time and costs. By summarizing and
analyzing these methods, we hope to have a better insight and provide guidance for future
directions.

Methods:
Up to now, a number of methods have been developed to predict the binding ability of
peptides to MHC based on various principles. Some of them employ matrix models or machine
learning models based on the sequence characteristic embedded in peptides or MHC to predict the
binding ability of peptides to MHC. Some others utilize the three-dimensional structural
information of peptides or MHC, for example, by extracting three-dimensional structural
information to construct a feature matrix or machine learning model, or directly using protein
structure prediction, molecular docking to predict the binding mode of peptides and MHC.

Results:
Although the methods in predicting peptide-MHC binding based on the feature matrix or
machine learning model can achieve high-throughput prediction, the accuracy of which depends
heavily on the sequence characteristic of confirmed binding peptides. In addition, it cannot provide
insights into the mechanism of antigen specificity. Therefore, such methods have certain
limitations in practical applications. Methods in predicting peptide-MHC binding based on
structural prediction or molecular docking are computationally intensive compared to the methods
based on feature matrix or machine learning model and the challenge is how to predict a reliable
structural model.

Conclusion:
This paper reviews the principles, advantages and disadvantages of the methods of
peptide-MHC binding prediction and discussed the future directions to achieve more accurate
predictions.
An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics
Authors: Rolfs Zach , Millikin Robert J. , Smith Lloyd M. 
Published: April 2020

Background:
The identification of non-specifically cleaved peptides in proteomics and
peptidomics poses a significant computational challenge. Current strategies for the identification of
such peptides are typically time-consuming and hinder routine data analysis.

Objective:
We aimed to design an algorithm that would improve the speed of semi- and nonspecific
enzyme searches and could be applied to existing search programs.

Methods:
We developed a novel search algorithm that leverages fragment-ion redundancy to
simultaneously search multiple non-specifically cleaved peptides at once. Briefly, a theoretical
peptide tandem mass spectrum is generated using only the fragment-ion series from a single
terminus. This spectrum serves as a proxy for several shorter theoretical peptides sharing the same
terminus. After database searching, amino acids are removed from the opposing terminus until the
observed and theoretical precursor masses match within a given mass tolerance.

Results:
The algorithm was implemented in the search program MetaMorpheus and found to
perform an order of magnitude faster than the traditional MetaMorpheus search and produce
superior results.

Conclusion:
We report a speedy non-specific enzyme search algorithm that is open-source and
enables search programs to utilize fragment-ion redundancy to achieve a notable increase in search
speed.