bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted Next-Generation Sequencing for Human Leukocyte Antigen Typing in a Clinical Laboratory: Metrics of Relevance and Considerations for Its Successful Implementation
Authors: Gandhi Manish J. , Ferriola Deborah , Huang Yanping , Duke Jamie L. , Monos Dimitri 
Published: February 2017

Context.—
Numerous feasibility studies to type human leukocyte antigens (HLAs) by next-generation sequencing (NGS) have led to the development of vendor-supported kits for HLA typing by NGS. Some clinical laboratories have introduced HLA-NGS, and many are investigating the introduction. Standards from accrediting agencies form the regulatory framework for introducing this test into clinical laboratories.

Objectives.—
To provide an assessment of metrics and considerations relevant to the successful implementation of clinical HLA-NGS typing, and to provide as a reference a validated HLA-NGS protocol used clinically since December 2013 at the Children's Hospital of Philadelphia (Philadelphia, Pennsylvania).

Data Sources.—
The HLA-NGS has been performed on 2532 samples. The initial 1046 and all homozygous samples were also typed by an alternate method. The HLA-NGS demonstrated 99.7% concordance with the alternate method. Ambiguous results were most common at the DPB1 locus because of a lack of phasing between exons 2 and 3 or the unsequenced exon 1 (533 of 2954 alleles; 18.04%) and the DRB1 locus because of not sequencing exon 1 (75 of 3972 alleles; 1.89%). No ambiguities were detected among the other loci. Except for 2 false homozygous samples, all homozygous samples (1891) demonstrated concordance with the alternate method. The article is organized to address the critical elements in the preanalytic, analytic, and postanalytic phases of introducing this assay into the clinical laboratory.

Conclusions.—
The results demonstrate that HLA typing by NGS is a highly accurate, reproducible, efficient method that provides more-complete sequencing information for the length of the HLA gene and can be the single methodology for HLA typing in clinical immunogenetics laboratories.
Minimum standards for ultrasound equipment in intensive care. Recommendations from CICM Ultrasound Special Interest Group
Authors: Costello Cartan , Yastrebov Konstantin , Yang Yang , Hilton Andrew , Vij Sanjiv , Orde Sam 
Published: February 2017

AbstractCritical care ultrasonography allows rapid bedside assessment and monitoring of severely ill patients. It provides important information on a real‐time basis for patients' management and clinical decision‐making, leading to improvements in delivered quality of care. Provision of this service is not possible without appropriate equipment. This document recommends minimum standards for ultrasound equipment required for use in intensive care units in Australia and New Zealand.
Regulation at multiple levels control the expression of folate transporters in liver cells in conditions of ethanol exposure and folate deficiency
Authors: Thakur Shilpa , Kaur Jyotdeep 
Published: February 2017

AbstractComplex regulatory mechanisms control the expression of folate transporters within cells. Liver is the primary reserve of the folate stores within the body. As excessive alcohol consumption or inefficient dietary folate intake are known to create folate deficiency, so therefore the current study was designed to explore various regulatory mechanisms controlling the expression of folate transport in liver cells in conditions of ethanol exposure and folate deficiency. In order to see whether the effects mediated by the treatments are reversible or not, ethanol removal, and folate repletion was done after ethanol exposure and folate deficiency treatment respectively. Folate deficiency resulted an increase, whereas ethanol treatment decreased the folic acid uptake within the cells. The alterations in folic acid uptake were in agreement with the observed changes in the expression of folate transporters. Ethanol exposure resulted an increase in promoter methylation of reduced folate carrier; however, folate deficiency had no effect. The effects produced by ethanol exposure and folate deficiency were found to be reversible in nature as depicted in case of ethanol removal and folate repletion group. Rate of synthesis of folate transporters was found to be increased whereas half lives of mRNA of folate transporters was found to be decreased on folate deficiency treatment and reverse was the case on ethanol treatment. Overall, alteration in the expression of folate transporters under ethanol exposure and folate deficient conditions can be attributed to those regulatory mechanisms which work at the mRNA level. © 2015 BioFactors, 41(4):232–241, 2015
Cafestol has a weaker inhibitory effect on osteoclastogenesis than kahweol and promotes osteoblast differentiation
Authors: Fukuma Yutaka , Sakai Eiko , Nishishita Kazuhisa , Okamoto Kuniaki , Tsukuba Takayuki 
Published: February 2017

AbstractBone homeostasis is regulated by a balance between osteoclast (OCL)‐mediated bone resorption and osteoblast (OBL)‐mediated bone formation. Thus, developing a compound that simultaneously inhibits OCL function and promotes OBL function would be useful as a new medical therapy for bone diseases. Here, we examined the effects of cafestol, a coffee diterpene, on the differentiation of OCLs and OBLs. Cafestol prevented OCL formation in a dose‐dependent manner and suppressed the bone‐resorbing activity of OCLs. Interestingly, the viability of OCLs treated with 10–50 µM cafestol was significantly higher than that of untreated cells. At the molecular level, cafestol markedly decreased RANKL‐induced phosphorylation of extracellular signal‐regulated kinase (Erk) and inhibitor of nuclear factor kappa B alpha (IκBα). Compared to kahweol, another coffee‐specific diterpene, the inhibitory effects of cafestol were milder on OCL differentiation, and cafestol and kahweol showed different characteristics in induction of the phase ΙΙ antioxidant enzymes and sensitivities in nuclear factor‐erythroid 2‐related factor 2 (Nrf2)‐deficient BMMs. In addition to inhibiting OCLs, cafestol enhanced the differentiation of osteoblastic cells by increasing the mRNA levels of differentiation markers. Thus, cafestol inhibits OCL differentiation and promotes OBL differentiation, suggesting that cafestol may be a novel agent for bone diseases. © 2015 BioFactors, 41(4):222–231, 2015
Metabolic responses to dietary leucine restriction involve remodeling of adipose tissue and enhanced hepatic insulin signaling
Authors: Wanders Desiree , Stone Kirsten P. , Dille Kelly , Simon Jacob , Pierse Alicia , Gettys Thomas W. 
Published: February 2017

AbstractDietary leucine was incrementally restricted to test whether limiting this essential amino acid (EAA) would fully reproduce the beneficial responses produced by dietary methionine restriction. Restricting leucine by 85% increased energy intake and expenditure within 5 to 7 days of its introduction and reduced overall accumulation of adipose tissue. Leucine restriction (LR) also improved glucose tolerance, increased hepatic release of fibroblast growth factor 21 into the blood stream, and enhanced insulin‐dependent activation of Akt in liver. However, LR had no effect on hepatic lipid levels and failed to lower lipogenic gene expression in the liver. LR did affect remodeling of white and brown adipose tissues, increasing expression of both thermogenic and lipogenic genes. These findings illustrate that dietary LR reproduces many but not all of the physiological responses of methionine restriction. The primary differences occur in the liver, where methionine and LR cause opposite effects on tissue lipid levels and expression of lipogenic genes. Altogether, these findings suggest that the sensing systems which detect and respond to dietary restriction of EAAs act through mechanisms that both leucine and methionine are able to engage, and in the case of hepatic lipid metabolism, may be unique to specific EAAs such as methionine. © 2015 BioFactors, 41(6):391–402, 2015
Effect of ZIP2 Gln/Arg/Leu (rs2234632) polymorphism on zinc homeostasis and inflammatory response following zinc supplementation
Authors: Giacconi Robertina , Costarelli Laura , Malavolta Marco , Cardelli Maurizio , Galeazzi Roberta , Piacenza Francesco , Gasparini Nazzarena , Basso Andrea , Mariani Erminia , Fulop Tamas , Rink Lothar , Dedoussis George , Herbein Georges , Jajte Jolanta , Provinciali Mauro , Busco Franco , Mocchegiani Eugenio 
Published: February 2017

AbstractZinc dyshomeostasis may lead to an augmented production of proinflammatory cytokines promoting chronic inflammation and increasing the susceptibility to age‐related diseases. Several studies suggest that the zinc transporter protein ZIP2 may play a relevant role in the immune system especially during zinc deficiency, while a polymorphism on the coding region of ZIP2 gene (Gln/Arg/Leu) has been associated with severe carotid artery disease. The aim of this study is to investigate the role of ZIP2 SNP on zinc and inflammatory status in 1090 elderly healthy free‐living subjects enrolled in the ZincAge project and to assess the effect of zinc supplementation on zinc status, inflammatory mediators, and zinc transporter expression depending on ZIP2 genotype. ZIP2 Leu− (Arg43Arg) carriers showed enhanced IL‐6, TNF‐α, and RANTES plasma levels associated with decreased free cytosolic zinc in PBMCs and an upregulation of zinc transporters ZIP2, ZIP8, and Znt1. Moreover, Leu− subjects displayed significant decrement of inflammatory mediators such as MCP‐1, TNF‐α, and RANTES following zinc supplementation. In summary, this investigation provides new evidence on the effect of ZIP2 Gln/Arg/Leu polymorphism on proinflammatory mediators and zinc homeostasis in elderly population with a more pronounced anti‐inflammatory effect of zinc supplementation in subjects carrying ZIP2 Leu− (Arg43Arg) genotype. These novel findings could be useful in identifying elderly subjects who may benefit of zinc intervention to decrease the inflammatory status and to prevent or delay the development of age‐related diseases. © 2015 BioFactors, 41(6):414–423, 2015
Hydrodeoxygenation of Phenol over Zirconia‐Supported Catalysts: The Effect of Metal Type on Reaction Mechanism and Catalyst Deactivation
Authors: Teles Camila A. , Rabelo‐Neto Raimundo C. , Jacobs Gary , Davis Burtron H. , Resasco Daniel E. , Noronha Fábio B. 
Published: February 2017

AbstractThis work aims at investigating the effect of the type of metal (Pt, Pd, Rh, Ru, Cu, Ni, Co) on the performance of ZrO2‐supported catalysts for the hydrodeoxygenation of phenol in the gas phase at 573 K and 1 atm. Two different reaction pathways take place depending on the type of the metal. For Pt/ZrO2 and Pd/ZrO2 catalysts, phenol is mainly tautomerized, followed by hydrogenation of the C=C bond of the tautomer intermediate formed, producing cyclohexanone and cyclohexanol. By contrast, the direct dehydroxylation of phenol followed by hydrogenolysis might also occur over more oxophilic metals such as Rh, Ru, Co, and Ni. In addition to the metals, the oxophilic sites of this support represented by Zr4+ and Zr3+ cations near the perimeter of the metal particles also increased the selectivity to deoxygenated products. All catalysts were significantly deactivated mainly owing to the growth of metal particle size and the decrease in the density of oxophilic sites.
Self‐Assembling Molecular Logic Gates Based on DNA Crossover Tiles
Authors: Campbell Eleanor A. , Peterson Evan , Kolpashchikov Dmitry M. 
Published: February 2017

AbstractDNA‐based computational hardware has attracted ever‐growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self‐assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions.
Simulation of the UV/Visible Absorption Spectra of Fluorescent Protein Chromophore Models
Authors: Zutterman Freddy , Liégeois Vincent , Champagne Benoît 
Published: February 2017

AbstractTime‐dependent density functional theory has been used to simulate the UV/Vis absorption spectra of fluorescent protein model chromophores with particular focus on the vibronic structure of the lowest‐energy absorption band as a structural fingerprint. Combining the B3LYP‐35 XC functional with non‐equilibrium solvation and the gradient approach provides a vibronic structure close to that recorded experimentally (when comparisons with experiment are possible). This study focuses on the chromophore present in green fluorescent proteins (FP1), in its neutral and deprotonated forms as well as for both cis (Z) and trans (E) conformations. The method was then employed to simulate the spectra of structures for which experimental spectra are not available or not well resolved. The effect of extending the conjugation of the chromophore, by adding unsaturated moieties such as in the chromophore of DsRed (FP2), was considered. Overall, among these three investigated structural modifications (neutral versus anionic, smaller versus larger chromophore, and cis versus trans conformations), absorption spectra can only distinguish unambiguously between the neutral and anionic forms. An extension of the π‐conjugation length of the chromophore is, as would be expected, reflected in a bathochromic shift of the absorption band maximum, but modifications of the chromophore environment in proteins can also induce shifts of the absorption maximum, and they are difficult to distinguish from each other.
The ecological significance of secondary seed dispersal by carnivores
Authors: Hämäläinen Anni , Broadley Kate , Droghini Amanda , Haines Jessica A. , Lamb Clayton T. , Boutin Stan , Gilbert Sophie 
Published: February 2017

AbstractAnimals play an important role in the seed dispersal of many plants. It is increasingly recognized, however, that the actions of a single disperser rarely determine a seed's fate and final location; rather, multiple abiotic or animal dispersal vectors are involved. Some carnivores act as secondary dispersers by preying on primary seed dispersers or seed predators, inadvertently consuming seeds contained in their prey's digestive tracts and later depositing viable seeds, a process known as diploendozoochory. Carnivores occupy an array of ecological niches and thus range broadly on the landscape. Consequently, secondary seed dispersal by carnivores could have important consequences for plant dispersal outcomes, with implications for ecosystem functioning under a changing climate and across disturbed landscapes where dispersal may be otherwise limited. For example, trophic downgrading through the loss of carnivores may reduce or eliminate diploendozoochory and thus compromise population connectivity for lower trophic levels. We review the literature on diploendozoochory and conclude that the ecological impact of a secondary vs. primary seed disperser depends on the relative dispersal distances, germination success, and the proportion of seeds exposed to secondary dispersal by carnivores. None of the studies up to present day have been able to rigorously assess the ecological significance of this process. We provide a framework of the components that determine the significance of diploendozoochory across systems and identify the components that must be addressed in future studies attempting to assess the ecological importance of diploendozoochory.
Reduced‐complexity simply/doubly differential primary synchronization for LTE systems
Authors: Nasraoui Leila , Najjar Atallah Leila , Siala Mohamed 
Published: February 2017

AbstractIn this paper, we address the problem of primary synchronization in Long Term Evolution (LTE) systems, and we assess the Frequency Offset (FO)–combating capabilities of the two studied reduced‐complexity approaches. We also provide a comparative study that covers computational complexity, time synchronization, and sector search performance considering multiple antenna configuration and under standardized channel models. The studied approaches, referred to as Simply Differential (SD) and Doubly Differential (DD) exploit Zadoff‐Chu (ZC) sequences to which differential correlation–based metrics are tailored. The SD approach computes differential correlation between the received samples and compensates the output with an adjustment frequency that depends on the training ZC sequence. This allows coarse time synchronization and sector search in a sole stage, which is a particular feature compared to most of the existing methods. The DD approach performs DD correlation of consecutive samples to detect a ZC sequence pattern within the received signal. To accomplish primary synchronization, it requires a second stage in which cross‐correlation is performed between the received signal and the local known ZC sequence candidates. This allows to identify the sector and helps to fine‐tune time synchronization. To assess their FO‐combatting capabilities, we examine the impact of an FO on the SD and DD metrics through theoretical analysis and simulation. The study shows the sensitivity of the SD approach to the FO and the immunity of the DD one. Simulation and numerical results prove the efficiency of the presented approaches under LTE standardized channel models and validate the analysis of the FO effect on time synchronization performance.
The crown joules: energetics, ecology, and evolution in humans and other primates
Authors: Pontzer Herman 
Published: February 2017

AbstractBiological diversity is metabolic diversity: Differences in anatomy, physiology, life history, and activity reflect differences in energy allocation and expenditure among traits and tasks. Traditional frameworks in primatology, human ecology, public health, and paleoanthropology view daily energy expenditure as being more variable within than between species, changing with activity level but essentially fixed for a given body size. Growing evidence turns this view on its head. Total energy expenditure (kcal/d), varies relatively little within species, despite variation in physical activity; it varies considerably among species even after controlling for the effect of body size. Embracing this emerging paradigm requires rethinking potential trade‐offs in energy allocation within and between species, assessing evidence of metabolic acceleration within lineages, and abandoning activity‐based estimates of total energy expenditure. Difficult and exciting work lies ahead in the effort to untangle the ecological and evolutionary pressures shaping primate metabolic diversity.
Intra‐bone marrow injection of trace elements co‐doped calcium phosphate microparticles for the treatment of osteoporotic rat
Authors: Yang Xianyan , Xu Sanzhong , Chen Xiaoyi , He Dongshuang , Ke Xiurong , Zhang Lei , Yang Guojing , Liu An , Mou Xiaozhou , Xia Wei , Gou Zhongru 
Published: February 2017

AbstractOsteoporotic femur fractures are the most common fragility fracture and account for approximately one million injuries per year. Local intervention by intra‐marrow injection is potentially a good choice for preventing osteoporotic bone loss when the osteoporotic femoral fracture was treated. Previously, it was shown that trace element co‐doped calcium phosphate (teCaP) implants could stimulate osteoporotic bone marrow mesenchymal stem cell activity in vitro and bone regeneration in femoral bone defects in osteoporotic animal models. They hypothesized that local intra‐marrow injection of teCaP particles could improve bone function because the teCaP can sustain release of biologically essential inorganic minerals and improve bone remodeling in osteoporosis. The teCaP and CaP particles were synthesized in simulated body fluid with and without adding silicon, zinc and strontium ions. Female rats (8 months) were ovariectomized (OVX) or sham‐operated, and then intervened in the femoral marrow space at 12 months old. Groups include: (1) saline water; (2) CaP particles; and (3) teCaP particles. After 2–3 months of intervention, the sham groups showed higher bone mineral density (MBD) in the femur, and teCaP group increased the BMD in the OVX groups. The compressive strength of the OVX‐teCaP group was significantly higher than that in the OVX‐CaP group. Significant differences between OVX‐teCaP and OVX‐CaP groups were found for bone mineral microarchitecture, bone mineral density, and trace mineral content, but not for feces composition. These results confirm the teCaP particles could suppress osteoporotic bone loss by local intramarrow injection. Therefore, this biomaterial could be used as a next‐generation combination treatment for osteoporotic trauma and osteoporosis itself. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1422–1432, 2017.
Flow cytometric analysis as an additional predictive tool of treatment response in children with chronic‐phase chronic myeloid leukemia treated with imatinib
Authors: Shima Haruko , Kiyokawa Nobutaka , Miharu Masashi , Tanizawa Akihiko , Kurosawa Hidemitsu , Watanabe Akihiro , Ito Masaki , Tono Chikako , Yuza Yuki , Muramatsu Hideki , Hotta Noriko , Okada Masahiko , Hamamoto Kazuko , Kajiwara Ryosuke , Saito Akiko M , Horibe Keizo , Mizutani Shuki , Adachi Souichi , Ishii Eiichi , Shimada Hiroyuki 
Published: February 2017

AbstractBone marrow samples of newly diagnosed children with chronic‐phase chronic myeloid leukemia (CML) were obtained at diagnosis and after imatinib initiation and stained with anti‐human CD34, CD38, CD123, CD45RA, cMpl, and lineage antibodies. Flow cytometric analysis revealed that granulocyte macrophage progenitor predominance in CML progenitors at diagnosis and elevated cMpl expression in bone marrow progenitors at 3 months may predict poor outcome in children with chronic‐phase CML treated with imatinib. We recommend flow cytometric analysis of bone marrow in the early phase of treatment, as it is a convenient tool that may predict treatment response and guide CML management.
Long‐term risk of portal hypertension and related complications in children treated with 6‐thioguanine for acute lymphoblastic leukemia: A single‐center experience
Authors: Roy Moulik Nirmalya , M Taj Mary 
Published: February 2017

AbstractLong‐term follow‐up of 11 children with 6‐thioguanine‐induced hepatoportal toxicity is described. Features of persistent portal hypertension in eight patients after 9.7 ± 3.4 years (mean ± SD) of treatment were more common in late presenters. Splenomegaly, thrombocytopenia and altered hepatic echotexture were seen in six, eight and seven patients, respectively. One of the thrombocytopenic patients had heavy menstrual bleeding and pregnancy loss. Five of six patients who underwent upper gastrointestinal endoscopy had esophageal varices and four underwent banding. Late presentation in a subset of patients mandates long‐term surveillance and follow‐up for all patients treated with 6‐thioguanine for early detection and management of hepatoportal complications.