Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining the Best of Both Worlds: A Semantic Web Book Mashup as a Linked Data Service Over CMS Infrastructure

We propose a proof-of-concept of how the best of the Web world (RESTful services, Semantic technologies, and CMSs) can be successfully incorporated in the form of a semantic mashup. This mashup enriches data from various Web APIs with semantics to produce personalized book recommendations and to make them available as Linked Data. It is shown that this approach not only leaves reasoning expressiveness and effective ontology management uncompromised but comes to their benefit. It also bears potential applications for libraries and cataloguing services that can take advantage of mashup merging, semantic personalization, and ranking of book records and reviews.
University of Birmingham Mitochondrial genome sequencing in mesolithic North East Europe unearths a new sub-clade within the broadly distributed human haplogroup C1

The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined ‘‘C1f’’. We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.
Performance evaluation of a new automated fourth-generation HIV Ag/Ab combination chemiluminescence immunoassay

*Corresponding author: Chuanmin Tao, Department of Laboratory Medicine/Clinical Research Center of Laboratory Medicine, West China Hospital of Sichuan University, No.37 GuoXue Alley, Chengdu, Sichuan 610041, P.R. China, Phone: +86-28-85422612, Fax: +86-28-85582944, E-mail: taocm@scu.edu. cn Yanhua Zhao, Yu Gou, Dongdong Li, Tingting Wang, Xiyue Huang and Mingqiao Shi: Department of Laboratory Medicine/Clinical Research Center of Laboratory Medicine, West China Hospital of Sichuan University, No.37 GuoXue Alley, Chengdu, Sichuan, P.R. China Letter to the Editor
Phosphate-induced metal stabilization: Use of apatite and bone char for the removal of soluble radionuclides in authentic and simulated DOE groundwater

The apatite group of minerals is a family of calcium phosphate phases. Apatite is the principal component of bone tissue, and it also occurs naturally as mineral deposits in the geosphere. Bone char is calcined (coked) animal bone, containing activated carbon as well as calcium phosphate mineral phases. Apatite II{trademark} is a more reactive form of apatite, supplied by UFA Ventures, Inc., at a cost of approximately 1/4 that of commercial bone char. Apatite is shown to be effective for the removal of select heavy metal impurities in groundwater. Previous investigations have demonstrated that apatite is an effective medium for the stabilization of soluble lead, cadmium, and zinc from mine waste leachate by the formation of highly insoluble precipitate phases. The performance of bone char and apatite II are compared with other candidate sorption media (including granular activated carbon and anion exchange resin) for the removal of soluble uranyl ion in synthetic DOE Site groundwater supplemented with varying levels of interfering nitrate ion. Apatite II has a greater affinity for U(VI), especially in the presence of nitrate ion, as evidenced by a larger value for the conditional distribution coefficient (Kd) in batch test experiments. Contact of uranyl nitrate solution withmore » apatite II is shown to produce highly insoluble mineral phases of the autunite group (calcium uranyl phosphate hydrates). Apatite II is also demonstrated to be moderately effective for the removal of soluble radioactive isotopes of strontium, but not cesium, when these ions are supplemented into authentic DOE Site groundwater. « less
Using Lean to Advance Quality Improvement Research

Introduction:Quality improvement research skills are not commonplace among quality improvement practitioners, and research on the effectiveness of quality improvement has not always kept pace with improvement innovation. However, the Lean tools applied to quality improvement should be equally relevant to the advancement of quality improvement research. Methods:We applied the Lean methods to develop a simplified quality improvement publication pathway enabling a small research methodology group to increase quality improvement research throughout the institution. The key innovations of the pathway are horizontal integration of the quality improvement research methods group across the institution, implementation of a Lean quality improvement research pathway, and application of a just-in-time quality improvement research toolkit. Results:This work provides a road map and tools for the acceleration of quality improvement research. At our institution, the Lean quality improvement research approach was associated with statistically significant increases in the number (annual mean increase from 3.0 to 8.5, p = .03) and breadth of published quality improvement research articles, and in the number of quality improvement research projects currently in process. Discussion:Application of Lean methods to the quality improvement research process can aid in increasing publication of quality improvement articles from across the institution.
MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. IMPORTANCE The initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants. IMPORTANCE The initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants.
The Rapalogue, CCI-779, Improves Salivary Gland Function following Radiation

The standard of care for head and neck cancer typically includes surgical resection of the tumor followed by targeted head and neck radiation. However depending on tumor location and stage, some cases may not require surgical resection while others may be treated with chemoradiation. Unfortunately, these radiation treatments cause chronic negative side effects for patients. These side effects are associated with damage to surrounding normal salivary gland tissue and include xerostomia, changes in taste and malnutrition. The underlying mechanisms of chronic radiation-induced salivary gland dysfunction are unknown, however, in rodent models persistently elevated proliferation is correlated with reduced stimulated salivary flow. The rapalogue, CCI-779, has been used in other cell systems to induce autophagy and reduce proliferation, therefore the aim of this study was to determine if CCI-779 could be utilized to ameliorate chronic radiation-induced salivary gland dysfunction. Four to six week old Atg5f/f; Aqp5-Cre, Atg5+/+; Aqp5-Cre and FVB mice were treated with targeted head and neck radiation. FVB mice were treated with CCI-779, chloroquine, or DMSO post-radiation. Stimulated salivary flow rates were determined and parotid and submandibular salivary gland tissues were collected for analyses. Mice with a defect in autophagy, via a conditional knockout of Atg5 in the salivary glands, display increased compensatory proliferation in the acinar cell compartment and hypertrophy at 24-72 hours following radiation. FVB mice treated with post-therapy CCI-779 have significant improvements in salivary gland physiology as determined by stimulated salivary flow rates, proliferation indices and amylase production and secretion. Consequently, post-radiation use of CCI-779 allows for improvement of salivary gland function and reestablishment of glandular homeostasis. As CCI-779 is already FDA approved for other uses, it could have a secondary use to alleviate the chronic side effects in head and neck cancer patients who have completed anti-tumor therapy.
Pregnancy and child health outcomes in pediatric and young adult leukemia and lymphoma survivors: a systematic review

Abstract As long-term survival is high for children and young adults diagnosed with leukemia and lymphoma, delineating maternal, fetal and offspring health risks is important to their family planning. This systematic review examined data comparing these health risks between leukemia and lymphoma survivors and women without a history of cancer. Following a search of Embase, PubMed, CINAHL, Cochrane, and Web of Science, 142 articles were screened and 18 were included in this review. No higher risks of spontaneous abortion, maternal diabetes and anemia, stillbirth, birth defects, or childhood cancer in offspring were observed in survivors compared to controls. Important to counseling and clinical care, live birth rates were lower, while preterm birth and low birth weight risks were modestly higher in survivors compared to controls. Findings were largely reassuring but highlight the lack of data on maternal cardiopulmonary risks, differential risk by cancer treatment type, and interventions to decrease these risks.
Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity

ABSTRACT Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
NeuroImage: Clinical Interindividual di ﬀ erences in motor network connectivity and behavioral response to iTBS in stroke patients

an of suggest that improvements in motor performance of the stroke-a ﬀ ected hand following modulation of primary motor cortex (M1) excitability by rTMS shows a high interindividual variability. We here tested the hypothesis that in stroke patients the interindividual variability of behavioral response to excitatory rTMS is related to interindividual di ﬀ erences in network connectivity of the stimulated region. Chronic stroke patients ( n = 14) and healthy controls ( n = 12) were scanned with functional magnetic re- sonance imaging (fMRI) while performing a simple hand motor task. Dynamic causal modeling (DCM) was used to investigate e ﬀ ective connectivity of key motor regions. On two di ﬀ erent days after the fMRI experiment, patients received either intermittent theta-burst stimulation (iTBS) over ipsilesional M1 or control stimulation over the parieto-occipital cortex. Motor performance and TMS parameters of cortical excitability were measured before and after iTBS. Our results revealed that patients with better motor performance of the a ﬀ ected hand showed stronger endogenous coupling between supplemental motor area (SMA) and M1 before starting the iTBS intervention. Applying iTBS to ipsilesional M1 signi ﬁ cantly increased ipsilesional M1 excitability and decreased contralesional M1 excitability as compared to control stimulation. Individual behavioral improvements fol- lowing iTBS speci ﬁ cally correlated with neural coupling strengths in the stimulated hemisphere prior to stimulation, especially for connections targeting the stimulated M1. Combining endogenous connectivity and behavioral parameters explained 82% of the variance in hand motor performance observed after iTBS. In conclusion, the data suggest that the individual susceptibility to iTBS after stroke is in ﬂ uenced by interindividual di ﬀ erences in motor network connectivity of the lesioned hemisphere.
Validation of a new surgical risk score for heart valve surgery: VMCP.

BACKGROUND Some studies have developed scores for the assessment of surgical risk, particularly the EuroSCORE, which, however, is complex and difficult to apply. We suggest a new and simpler score, which is more appropriate for the clinical practice and for the assessment of surgical risk in patients with heart valve diseases. OBJECTIVE This study was conducted to create and validate a simple and practical score to predict mortality and morbidity related to heart valve surgery. METHODS Hospital data from 764 patients were collected, and the score was validated using two statistical models: death (= mortality) and length of hospital stay (LHS) > 10 days (= morbidity). The score was composed by four indexes (V [heart valve lesion], M [myocardial function], C [coronary artery disease], and P [pulmonary artery pressure]). A cut-off point was set for the score, and uni and multivariate analyses were performed to confirm whether the score would be able to predict mortality and morbidity. The existence of association with other risk factors was also studied. RESULTS The score was validated with good internal consistency (0.65), and the best cut-off point for mortality and morbidity was 8. Scores > 8 can predict LHS > 10 days (odds ratio [OR] = 1.7; p = 0.006) and a higher death risk, at least in the univariate analysis (p = 0.049). However, the death risk could not be predicted in the multivariate analysis (p=0.258). CONCLUSION VMCP scores > 8 can predict LHS > 10 days and may be used as a new tool for the follow-up of patients with heart valve disease undergoing surgery.
Initial Experience of Single-port Laparoscopic Multivisceral Resection for Locally Advanced Colon Cancer

Aim:The aim of this study was to evaluate the safety and feasibility of single-port laparoscopic multivisceral resection (SLMVR) for locally advanced colon cancer invading or adhering to neighboring organs. Method:A prospectively collected database was collated of all patients undergoing SLMVR from January 2011 to December 2014. Short-term and long-term oncologic outcomes were evaluated. Results:Thirty consecutive patients who underwent SLMVR were identified and the completion rate was 90%. The R0 resection rate of the primary tumor was 100%. The postoperative complication rate was 23.3%. The 3-year relapse-free survival rates of patients with stage II (n=11) and stage III (n=12) disease were 80.8% and 54.6%, respectively. The 5-year overall survival rates of patients with stage II and stage III disease were 75.8% and 75.0% over a median follow-up of 42 months, respectively. Conclusions:SLMVR for locally advanced colon cancer is safe and feasible in selected patients.
The Effect of Vitamin D Supplementation on Breast Density Changes: A Clinical Trial Study

ABSTRACT The aim of this study was to determine the effect of supplementation with 50,000 IU/monthly vitamin D for 1 yr on breast density in Iranian women. Methods: This double-blind, placebo-controlled, single center clinical trial was conducted among 400 women aged 40 yr and older. Participants were allocated to 2 groups. Group 1 received vitamin D (Cholecalciferol) 50,000 IU in tablet form, monthly, for 1 yr. Group 2 received vitamin E 400 IU in tablet form, monthly, for the same period of time. Participants had follow-up clinic visits every 6 mo and received an annual mammogram. Results: Final data were evaluated based on 216 and 194 women in the vitamin D and control groups. The mean decrease in mammographic density was −5.01%(95% CI, −9.9% to −0.01%) and −2.34 %(95% CI, −6.84% to −2.15%) in the vitamin D and control groups, respectively. There was no significant association between vitamin D consumption and breast density after 1 yr (OR = 0.7, 95% CI, 0.46 to 1.06; P = 0.1). Similar results were observed when multivariate model of logistic regression analysis was performed. Conclusions: This study showed that monthly consumption of 50,000 IU of vitamin D supplementation for 1 yr did not affect breast density.
The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding

Significance The valley of Tehuacán in Mexico is an important center of early Mesoamerican agriculture. To characterize the genetic constitution of the earliest phase of maize cultivation, we reexamined San Marcos cave in Tehuacán and sequenced DNA from three newly discovered maize samples dating at a similar age of 5,000 y B.P. The genomes of these samples reveal unforeseen levels of genetic diversity as compared with modern maize, indicating that the effects of domestication were not yet complete. We find that their genetic constitution was similar and influenced by inbreeding, suggesting that the corresponding plants come from a reduced population of isolated and perhaps self-pollinated individuals. Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens dating at a similar age of 5,300–4,970 calibrated y B.P. On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, we show herein that the earliest maize from San Marcos cave was a partial domesticate diverging from the landraces and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci, such as teosinte branched1 (tb1) and brittle endosperm2 (bt2), had already lost most of the nucleotide variability present in Balsas teosinte, others, such as teosinte glume architecture1 (tga1) and sugary1 (su1), conserved partial levels of nucleotide variability that are absent from extant maize. Genetic comparisons among three temporally convergent samples revealed that they were homozygous and identical by descent across their genome. Our results indicate that the earliest maize from San Marcos was already inbred, opening the possibility for Tehuacán maize cultivation evolving from reduced founder populations of isolated and perhaps self-pollinated individuals.