bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recapitulation of gametic DNA methylation and its post-fertilization maintenance with reassembled DNA elements at the mouse Igf2/H19 locus
Authors: Matsuzaki Hitomi , Kuramochi Daichi , Okamura Eiichi , Hirakawa Katsuhiko , Ushiki Aki , Tanimoto Keiji 
Published: January 2020

AbstractBackgroundPaternal allele-specific DNA methylation of theH19imprinting control region (ICR) regulates imprinted expression of theIgf2/H19genes. The molecular mechanism by which differential methylation of theH19ICR is established during gametogenesis and maintained after fertilization, however, is not fully understood. We previously showed that a 2.9-kbH19ICR fragment in transgenic mice was differentially methylated only after fertilization, demonstrating that two separable events, gametic and post-fertilization methylation, occur at theH19ICR. We then determined that CTCF/Sox-Oct motifs and the 478-bp sequence of theH19ICR are essential for maintaining its maternal hypomethylation status and for acquisition of paternal methylation, respectively, during the post-fertilization period.ResultsUsing a series of 5′-truncatedH19ICR transgenes to dissect the 478-bp sequence, we identified a 118-bp region required for post-fertilization methylation activity. Deletion of the sequence from the paternal endogenousH19ICR caused loss of methylation after fertilization, indicating that methylation activity of the sequence is required to protect endogenousH19ICR from genome-wide reprogramming. We then reconstructed a synthetic DNA fragment in which the CTCF binding sites, Sox-Oct motifs, as well as the 118-bp sequence, were inserted into lambda DNA, and used it to replace the endogenousH19ICR. The fragment was methylated during spermatogenesis; moreover, its allele-specific methylation status was faithfully maintained after fertilization, and imprinted expression of the bothIgf2andH19genes was recapitulated.ConclusionsOur results identified a 118-bp region within theH19ICR that is required for de novo DNA methylation of the paternally inheritedH19ICR during pre-implantation period. A lambda DNA-based artificial fragment that contains the 118-bp sequence, in addition to the previously identifiedciselements, could fully replace the function of theH19ICR in the mouse genome.
Occurrence of abscesses during treatment with pazopanib in metastatic renal cancer: a case report
Authors: Puliafito Ivana , Russo Alessio , Sciacca Dorotea , Puglisi Caterina , Giuffrida Dario 
Published: January 2020

Abstract
Background
Pazopanib is a multitarget tyrosine kinase inhibitor used in the treatment of renal cancer and soft tissue sarcoma. Its use is commonly associated with a number of side effects, such as hemorrhagic diathesis, neutropenia, leukopenia, thrombocytopenia, nausea, vomiting, abdominal pain, increased serum aspartate aminotransferase, increased serum alanine aminotransferase, decreased serum glucose, increased serum bilirubin, decreased serum phosphate and magnesium, fatigue, hypertension, diarrhea, anorexia, proteinuria, and hypothyroidism. Abscesses of metastases caused by pazopanib administration are rarely reported in the literature.

Case presentation
We report a case of abscesses of lung metastases related to pazopanib in a patient with metastatic renal cancer. The patient was a 53-year-old Caucasian man who developed abscesses of lung metastases during the first 3 months of treatment with pazopanib. The abscesses resolved after 1 month by stopping pazopanib and administering adequate antibiotic therapy.

Conclusions
We conclude that abscesses of metastases could be a rare side effect occurring during treatment with pazopanib in patients with renal cancer.
SeXY chromosomes and the immune system: reflections after a comparative study
Authors: Meester Irene , Manilla-Muñoz Edgar , León-Cachón Rafael B. R. , Paniagua-Frausto Gustavo A. , Carrión-Alvarez Diego , Ruiz-Rodríguez C. Orelli , Rodríguez-Rangel Ximena , García-Martínez Joyce M. 
Published: January 2020

AbstractBackgroundSex bias in immune function has been contributed in part to a preponderance of immune system-related genes (ISRG) on the X-chromosome. We verified whether ISRG are more abundant on the X chromosome as compared to autosomal chromosomes and reflected on the impact of our findings.MethodsConsulting freely accessible databases, we performed a comparative study consisting of three complementary strategies. First, among coding X/Y-linked genes, the abundance of ISRG was compared to the abundance of genes dedicated to other systems. Genes were assigned considering three criteria: disease, tissue expression, and function (DEF approach). In addition, we carried out two genome-wide approaches to compare the contribution of sex and autosomal chromosomes to immune genes defined by an elevated expression in lymphatic tissues (LTEEG approach) or annotation to an immune system process, GO:0002376 (GO approach).ResultsThe X chromosome had less immune genes than the median of the autosomal chromosomes. Among X-linked genes, ISRG ranked fourth after the reproductive and nervous systems and genes dedicated to development, proliferation and apoptosis. On the Y chromosome, ISRG ranked second, and at the pseudoautosomal region (PAR) first. According to studies on the expression of X-linked genes in a variety of (mostly non-lymphatic) tissues, almost two-thirds of ISRG are expressed without sex bias, and the remaining ISRG presented female and male bias with similar frequency. Various epigenetic controllers, X-linkedMSL3and Y-linkedKDM5DandUTY,were preferentially expressed in leukocytes and deserve further attention for a possible role in sex biased expression or its neutralisation.ConclusionsThe X chromosome is not enriched for ISRG, though particular X-linked genes may be responsible for sex differences in certain immune responses. So far, there is insufficient information on sex-biased expression of X/Y-linked ISRG in leukocytes to draw general conclusions on the impact of X/Y-linked ISRG in immune function. More research on the regulation of the expression X-linked genes is required with attention to 1) femaleandmale mechanisms that may either augment or diminish sex biased expression and 2) tissue-specific expression studies.
A comparison of biofiltration performance based on bacteria and fungi for treating toluene vapors from airflow
Authors: Ghasemi Roohollah , Golbabaei Farideh , Rezaei Sasan , Pourmand Mohammad Reza , Nabizadeh Ramin , Jafari Mohammad Javad , masoorian Ensieh 
Published: January 2020

AbstractWith increasing concerns about industrial gas contaminants and the growing demand for durable and sustainable technologies, attentions have been gradually shifted to biological air pollution controls. The ability of Pseudomonas putida PTCC 1694 (bacteria) and Pleurotus ostreatus IRAN 1781C (fungus) to treat contaminated gas stream with toluene and its biological degradation was compared under similar operating conditions. For this purpose, a biofilter on the laboratory scale was designed and constructed and the tests were carried out in two stages. The first stage, bacterial testing, lasted 20 days and the second stage, fungal testing, lasted 16 days. Inlet loading rates (IL) for bacterial and fungal biofilters were 21.62 ± 6.04 and 26.24 ± 7.35 g/m3 h respectively. In general, fungal biofilter showed a higher elimination capacity (EC) than bacterial biofilter (18.1 ± 6.98 vs 13.7 ± 4.7 g/m3 h). However, the pressure drop in the fungal biofilter was higher than the bacterial biofilter (1.26 ± 0.3 vs 1 ± 0.3 mm water), which was probably due to the growth of the mycelium. Fungal biofiltration showed a better performance in the removal of toluene from the air stream.
Existence of solutions for a system of singular sum fractional q-differential equations via quantum calculus
Authors: Samei Mohammad Esmael 
Published: January 2020

AbstractIn this study, we discuss the existence of positive solutions for the system ofm-singular sum fractionalq-differential equations$$ \begin{gathered} D_{q}^{\alpha_{i}} x_{i} + g_{i} \bigl(t, x_{1}, \ldots, x_{m}, D_{q}^{\gamma _{1}} x_{1}, \ldots, D_{q}^{\gamma_{m}} x_{m} \bigr) \\ \quad{} +h_{i} \bigl(t, x_{1}, \ldots, x_{m}, D_{q}^{\gamma_{1}} x_{1}, \ldots, D_{q}^{\gamma_{m}} x_{m} \bigr)=0 \end{gathered} $$Dqαixi+gi(t,x1,…,xm,Dqγ1x1,…,Dqγmxm)+hi(t,x1,…,xm,Dqγ1x1,…,Dqγmxm)=0with boundary conditions$x_{i}(0) = x_{i}' (1) = 0$xi(0)=xi′(1)=0and$x_{i}^{(k)}(t) = 0$xi(k)(t)=0whenever$t=0$t=0, here$2\leq k \leq n-1$2≤k≤n−1, where$n= [\alpha_{i}]+ 1$n=[αi]+1,$\alpha_{i} \geq2$αi≥2,$\gamma_{i} \in(0,1)$γi∈(0,1),$D_{q}^{\alpha}$Dqαis the Caputo fractionalq-derivative of orderα, here$q \in(0,1)$q∈(0,1), function$g_{i}$giis of Carathéodory type,$h_{i}$hisatisfy the Lipschitz condition and$g_{i} (t , x_{1}, \ldots, x_{2m})$gi(t,x1,…,x2m)is singular at$t=0$t=0, for$1 \leq i \leq m$1≤i≤m. By means of Krasnoselskii’s fixed point theorem, the Arzelà-Ascoli theorem, Lebesgue dominated theorem and some norms, the existence of positive solutions is obtained. Also, we give an example to illustrate the primary effects.
The proteome of IVF-induced aberrant embryo-maternal crosstalk by implantation stage in ewes
Authors: Yang Qianying , Fu Wei , Wang Yue , Miao Kai , Zhao Haichao , Wang Rui , Guo Min , Wang Zhilong , Tian Jianhui , An Lei 
Published: January 2020

Abstract
Background
Implantation failure limits the success of in vitro fertilization and embryo transfer (IVF-ET). Well-organized embryo-maternal crosstalk is essential for successful implantation. Previous studies mainly focused on the aberrant development of in vitro fertilized (IVF) embryos. In contrast, the mechanism of IVF-induced aberrant embryo-maternal crosstalk is not well defined.

Results
In the present study, using ewes as the model, we profiled the proteome that features aberrant IVF embryo-maternal crosstalk following IVF-ET. By comparing in vivo (IVO) and IVF conceptuses, as well as matched endometrial caruncular (C) and intercaruncular (IC) areas, we filtered out 207, 295, and 403 differentially expressed proteins (DEPs) in each comparison. Proteome functional analysis showed that the IVF conceptuses were characterized by the increased abundance of energy metabolism and proliferation-related proteins, and the decreased abundance of methyl metabolism-related proteins. In addition, IVF endometrial C areas showed the decreased abundance of endometrial remodeling and redox homeostasis-related proteins; while IC areas displayed the aberrant abundance of protein homeostasis and extracellular matrix (ECM) interaction-related proteins. Based on these observations, we propose a model depicting the disrupted embryo-maternal crosstalk following IVF-ET: Aberrant energy metabolism and redox homeostasis of IVF embryos, might lead to an aberrant endometrial response to conceptus-derived pregnancy signals, thus impairing maternal receptivity. In turn, the suboptimal uterine environment might stimulate a compensation effect of the IVF conceptuses, which was revealed as enhanced energy metabolism and over-proliferation.

Conclusion
Systematic proteomic profiling provides insights to understand the mechanisms that underlie the aberrant IVF embryo-maternal crosstalk. This might be helpful to develop practical strategies to prevent implantation failure following IVF-ET.
Detection of bladder cancer using urinary cell‐free DNA and cellular DNA
Authors: Ou Zhenyu , Li Kai , Yang Ting , Dai Ying , Chandra Mohan , Ning Jun , Wang Yongli , Xu Ran , Gao Tangjie , Xie Yu , He Qing , Li Yuanwei , Lu Qin , Wang Long , Song Zhuo 
Published: January 2020

AbstractBackgroundThe present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell‐free DNA (cfDNA) from urine supernatant or cellular DNA from urine sediments of hematuria patients. A panel of 48 bladder cancer‐specific genes was selected. A next‐generation sequencing‐based assay with a cfDNA barcode‐enabled single‐molecule test was employed. Mutation profiles of blood, urine, and tumor sample from 16 bladder cancer patients were compared. Next, urinary cellular DNA and cfDNA were prospectively collected from 125 patients (92 bladder cancer cases and 33 controls) and analyzed using the 48‐gene panel. The individual gene markers and combinations of markers were validated according to the pathology results. The mean areas under the receiver operating characteristic (ROC) curves (AUCs) obtained with the various modeling approaches were calculated and compared.ResultsThis pilot study of 16 bladder cancer patients demonstrated that gene mutations in urine supernatant and sediments had better concordance with cancer tissue as compared with plasma. Logistic analyses suggested two powerful combinations of genes for genetic diagnostic modeling: five genes for urine supernatant (TERT, FGFR3, TP53, PIK3CA, and KRAS) and seven genes for urine sediments (TERT, FGFR3, TP53, HRAS, PIK3CA, KRAS, and ERBB2). The accuracy of the five‐gene panel and the seven‐gene panel in the validation cohort yielded AUCs of 0.94 [95% confidence interval (CI) 0.91–0.97] and 0.91 (95% CI 0.86–0.96), respectively. With the addition of age and gender, the diagnostic power of the urine supernatant five‐gene model and the urine sediment seven‐gene model improved as the revised AUCs were 0.9656 (95% CI 0.9368–0.9944) and 0.9587 (95% CI 0.9291–0.9883).ConclusionscfDNA from urine bears great diagnostic potential. A five‐gene panel for urine supernatant and a seven‐gene panel for urine sediments are promising options for identifying bladder cancer in hematuria patients.
Comprehensive approaches to addressing mental health needs and enhancing school security: a hybrid type II cluster randomized trial
Authors: Eisman Andria B. , Heinze Justin , Kilbourne Amy M. , Franzen Susan , Melde Christopher , McGarrell Edmund 
Published: January 2020

Abstract
Background
School safety is fundamental to fostering positive outcomes for children. Violence remains a critical public health issue with 8.1% of elementary and 21.8% of middle school students reporting daily or weekly bullying in 2015–16. Similarly, over half of lifetime mental health concerns become evident before age 14. Thus, elementary school is a key time for comprehensive school safety interventions. Yet, interventions are rarely delivered with fidelity in community settings. Evidence-based interventions must be complemented by implementation strategies to achieve desired public health outcomes.

Methods
We develop and test an intervention focused on promoting a positive school climate guided by a school-based 3-person leadership team (3-PLT) using a hybrid Type II design. The 3-PLT includes a School Resource Officer, (SRO), administrator and mental health services professional as a newly appointed climate specialist (CS). The interventions to be delivered include 1) Restorative justice, 2) Mental Health First Aid and 3) Crime Prevention Through Environmental Design. The CS will lead the team and coordinate implementation through a process of interactive problem solving and supports, consistent with the implementation facilitation strategy. We will conduct a cluster randomized controlled trial with staged entry over two school years in Genesee County, Michigan (n = 20 elementary schools, with 10 participating per school year). We will use a combination of data sources including data collected by schools (e.g., discipline data), a student survey, and a teacher survey. We will also conduct a process evaluation and assess implementation and sustainability through focus groups with key stakeholders, teachers, and students. Finally, we will conduct a cost-benefit analysis.

Discussion
Results from both the behavioral outcome and implementation strategy evaluations are expected to have significant implications for school safety and student well-being. This study adopts a unique approach by integrating three evidence-based programs and incorporating implementation facilitation led by the CS as part of the 3-PLT to support intervention delivery and enhance public health impact among schools in disadvantaged communities with students at risk of poor health outcomes. This study aims to create a comprehensive, well-integrated model intervention that is sustainable and can be translated to similar high-risk settings.

Trial registration
Trial was retrospectively registered, registration ISRCTN1226421, May 16, 2019.
Practicing transformative planning: the territory-landscape plan as a catalyst for change
Authors: Albrechts Louis , Barbanente Angela , Monno Valeria 
Published: January 2020

AbstractThis paper advocates the need for transformative planning practices to cope with contemporary crises of climate change and intensifying economic inequality that regions, city-regions, and cities are increasingly confronted with. In-depth examination of planning processes is useful to grasp some crucial promises and problems of transformative planning and open up new possibilities for practice. Accordingly, the paper includes an investigation into the Territory-Landscape plan-making process developed in the Apulia region, Italy. This explicitly and intentionally aimed at promoting a radical discontinuity in regional planning culture and practice by changing the well-established relationship between territory-landscape protection and spatial planning. The process revealed that ‘landscape’ could function as a constructive picklock for proposing an alternative to the development-as-growth model firmly entrenched in the region, and envisioning desirable futures focused on the concept of ‘local self-sustainable development’. This implies subverting the hegemony of the ‘economic’ that has reduced dwellers to consumers, and the territory to a mere physical support for any kind of land transformation and urban development which exclude dwellers participation. Using the lens of transformative theory and building on an interpretive research approach that included also direct experience, the paper provides insights on changes in vision and concepts, discourses and practices, approach and instruments experienced in such a planning process. In conclusion, it reflects on lessons learned, and highlights some difficulties and contradictions with which the way towards transformative planning is paved for researchers engaged in turning their ideas into significant achievements in the real world.
The value of DWI in predicting the response to synchronous radiochemotherapy for advanced cervical carcinoma: comparison among three mathematical models
Authors: Zhang Hui , Zhou Yuyang , Li Jie , Zhang Pengjuan , Li Zhenzhen , Guo Junwu 
Published: January 2020

Abstract
Background
Diffusion weighted imaging(DWI) mode mainly includes intravoxel incoherent motion (IVIM), stretched exponential model (SEM) and Gaussian diffusion model, but it is still unclear which mode is the most valuable in predicting the response to radiochemotherapy for cervical cancer. This study aims to compare the values of three mathematical models in predicting the response to synchronous radiochemotherapy for cervical cancer.

Methods
Eighty-four patients with cervical cancer were enrolled into this study. They underwent DWI examination by using 12 b-values prior to treatment. The imaging parameters were calculated on the basis of IVIM, SEM and Gaussian diffusion models respectively. The imaging parameters derived from three mathematical modes were compared between responders and non-responders groups. The repeatability of each imaging parameter was assessed.

Results
The ADC, D or DDC value was lower in responders than in non-responders groups (P = 0.03, 0.02, 0.01). The α value was higher in responders group than in non-responders group (P = 0.03). DDC had the largest area under curves (AUC) (=0.948) in predicting the response to treatment. The imaging parameters derived from SEM had better repeatability (CCC for DDC and α were 0.969 and 0.924 respectively) than that derived from other exponential models.

Conclusion
Three exponential modes of DWI are useful for predicting the response to radiochemotherapy for cervical cancer, and SEM may be used as a potential optimal model for predicting treatment effect.
Effect of regional factor productivity on manufacturing sector: The case of Sino-Pak economic ties
Authors: Imran Muhammad , HuSen An , Kaleem Muhammad , Bangash Arshad Khan , Din Nizam Ud , Sobia  
Published: January 2020

Abstract
Introduction
Economic ties and trade blocs increase the flow of trade between participating countries and lead to different levels of economic and structural changes.

Case description
This paper focuses on the structure of industrial value-added between China and Pakistan, as the two countries recently launched the CPEC (China-Pakistan Economic Corridor) project.

Discussion and evaluation
This study utilizes panel data from 1995 to 2015 to test certain factor effects on regional value-added through econometric analyses. The results show that each country has its own economic growth rate and market size that respond differently to industrial value-added production.

Conclusion
Aggregate factor productivity at China is higher than in Pakistan but growth in factor productivity in the latter is higher than the former; similarly, the share of bilateral trade is higher in the case of Pakistan. Although each country responds differently to the new economic ties, the macroeconomic results support bilateral economic ties between them.
Research on a bifurcation location algorithm of a drainage tube based on 3D medical images
Authors: Pan Qiuling , Zhu Wei , Zhang Xiaolin , Chang Jincai , Cui Jianzhong 
Published: January 2020

AbstractBased on patient computerized tomography data, we segmented a region containing an intracranial hematoma using the threshold method and reconstructed the 3D hematoma model. To improve the efficiency and accuracy of identifying puncture points, a point-cloud search arithmetic method for modified adaptive weighted particle swarm optimization is proposed and used for optimal external axis extraction. According to the characteristics of the multitube drainage tube and the clinical needs of puncture for intracranial hematoma removal, the proposed algorithm can provide an optimal route for a drainage tube for the hematoma, the precise position of the puncture point, and preoperative planning information, which have considerable instructional significance for clinicians.
Ethnobiology of algarroba beer, the ancestral fermented beverage of the Wichí people of the Gran Chaco I: a detailed recipe and a thorough analysis of the process
Authors: Herrera Cano Anahí Naymé , Suárez María Eugenia 
Published: January 2020

AbstractAlgarroba (Prosopis alba) beer, known asaloja de algarroba(abbreviatedaloja) in local Spanish, is the ancestral alcoholic beveragepar excellenceof the Wichís and other indigenous peoples of South American Gran Chaco, but nowadays is in disuse. Mentions on the recipe exist, but they are relatively few, concise and/or partial, and most of them were not registered within ethnobiological studies. The aims of this study were to (a) describe in detail the preparation process of algarroba beer and (b) analyse the process from a holistic approach, integrating Wichí concepts and biological explanations. Any morphological type ofProsopis albafruits is useful, except those with poor mesocarp.Alojamust be prepared from relative fresh fruits, ground into pieces and not from flour alone. Through the senses, mainly taste and smell, the procedure is followed until optimal fermentation time is reached, which occurs at 24–48 h. Whenalojais ready, it tastestapay(bitter-sour) ornusuy(sour-salty). From the Wichí perspective, fermentation is both a maturation and a cooking process, and it is the “strength” (qahay,qahnayaj) of the pods, an intrinsic property, which allows fermentation to occur, with alcohol production. All interviewees’ remarks about the recipe are also explained by microbiological concepts. Altogether, results expand the knowledge on Wichí ethnobiology and are also useful to other disciplines interested in traditional food systems. Besides, they constitute a contribution to the rescue of the know-how on this traditional beverage for future generations and ultimately to food sovereignty.