bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing communication in algebraic multigrid using additive variants
Authors: Vassilevski Panayot S. , Yang Ulrike Meier 
Published: February 2014

SUMMARYAlgebraic multigrid (AMG) has proven to be an effective scalable solver on many high performance computers; however, its increasing communication complexity on coarser levels has shown to seriously impact its performance on computers with high communication cost. Additive AMG variants provide not only increased parallelism as well as decreased numbers of messages per cycle but also generally exhibit slower convergence. We present various new additive variants with convergence rates that are significantly improved compared to the classical additive algebraic multigrid method and investigate their potential for decreased communication, and improved communication‐computation overlap, features that are essential for good performance on future exascale architectures. Published 2014. This article is a US Government work and is in the public domain in the USA.
A Bioarchaeological and Biogeochemical Study of Warfare and Mobility in Andahuaylas, Peru (ca. ad 1160–1260)
Authors: Kurin D. S. , Lofaro E. M. , Gómez Choque D. E. , Krigbaum J. 
Published: February 2014

AbstractWarfare impacts how people and populations can move about the landscape. Ethnographers have posited that internal warfare, conflict that takes place within a single society, is strongly associated with female abduction. In contrast, external warfare, combat between different societies, is often accompanied by the in‐migration of men for purposes of defence. To test this assertion, we evaluate human remains from one of the most violent eras in Andean prehistory, the Late Intermediate Period (ad 1000–1400). In the south‐central highlands of Andahuaylas, Peru, this era witnessed the coalescence of two formidable polities, the Chanka and the Quichua. Ethnohistoric accounts describe internal warfare among the Chanka and external warfare between the Quichua and their neighbours. In this study, bioarchaeological and biogeochemical methods are marshalled to elucidate ancient patterns of violence and mobility with greater nuance. We employ strontium isotope analysis of tooth enamel apatite to inform on residential origin, and we reconstruct patterns of violent conflict through analysis of cranial trauma. In all, 265 crania were excavated from 17 cave ossuaries at two Chanka sites and one Quichua site. Data were collected on age, sex and cranial modification—an indicator of social identity and cranial trauma. A representative subsample of molars from 34 individuals subjected to strontium isotope analysis demonstrates that among the Chanka, violence was significantly directed towards social groups within society, marked by modified crania. The presence of two nonlocal women with signs of increased morbidity and mistreatment points to possible mobility‐by‐abduction. In contrast, among the Quichua, men have significantly more trauma, and wounds are concentrated on the anterior. Trauma on women is lower, nonlethal, and concentrated on the posterior. This divergent pattern is commonly observed in external warfare (raids and community defence), where men face attackers and women escape them. The presence of two nonlocal men supports a mobility model of strategic in‐migration. In sum, osteological and isotopic data sets are shown to reveal divergent life‐course experiences not captured by the archaeological data or historic records alone. Copyright © 2014 John Wiley & Sons, Ltd.
Ambient air pollution and the prevalence of obesity in chinese children: The seven northeastern cities study
Authors: Dong Guang‐Hui , Qian Zhengmin (Min) , Liu Miao‐Miao , Wang Da , Ren Wan‐Hui , Flick Louise H. , Fu John , Wang Jing , Chen Weiqing , Simckes Maayan , Trevathan Edwin 
Published: February 2014

ObjectiveThe association between air pollution and the prevalence of overweight and obesity is evaluated.MethodsThe population consisted of 30,056 children (aged 2‐14 years), randomly selected from 25 districts in Northeast China. Child weight and height were measured, and exposures to particulate matter with an aerodynamic diameter ≤10 μm (PM10), sulfur dioxide (SO2), nitrogen dioxides (NO2), and Ozone (O3) were estimated from the data collected at monitoring stations in the 25 districts. Using two‐level logistic models, we examined the association between the exposure and the prevalence of overweight and obesity.ResultsAmong the study children, 12.3% (3,704) were overweight and 14.1% (4,233) were obese. After adjusting for confounding factors, an increased prevalence of obesity was associated with an interquartile range increase in PM10 (31 μg/m3 ; odds ratio [ORs] = 1.19; 95% confidence interval [CI]: 1.11‐1.26), SO2 (7.4 ppb; ORs = 1.11; 95% CI: 1.03‐1.20), NO2 (5.3 ppb; ORs = 1.13; 95% CI: 1.04‐1.22), and O3 (11.5 ppb; ORs = 1.14; 95% CI: 1.04‐1.24). Prevalence of overweight increased with an interquartile range increase in O3 (11.5 ppb; ORs = 1.09; 95% CI: 1.03‐1.15).ConclusionsThis study suggests that air pollution is positively associated with an increased likelihood of obesity or overweight in children.
Pilot trial of risk‐adapted cyclophosphamide intensity based conditioning and HLA matched sibling and unrelated cord blood stem cell transplantation in newly diagnosed pediatric and adolescent recipients with acquired severe aplastic anemia
Authors: McGuinn Catherine , Geyer Mark B. , Jin Zhezhen , Garvin James H. , Satwani Prakash , Bradley M. Brigid , Bhatia Monica , George Diane , Duffy Deirdre , Morris Erin , van de Ven Carmella , Schwartz Joseph , Baxter‐Lowe Lee Ann , Cairo Mitchell S. 
Published: February 2014

BackgroundCyclophosphamide‐based conditioning regimens and allogeneic hematopoietic stem cell transplantation (AlloHSCT) from matched related donors (MRD) has resulted in the highest survival rates in children and adolescents with acquired severe aplastic anemia (SAA). Time to transplant has consistently been associated with decreased overall survival. Reduced toxicity conditioning and AlloHSCT has been used successfully in other pediatric non‐malignant diseases.ProcedureWe piloted a risk‐adapted AlloHSCT approach, using fludarabine and anti‐thymocyte globulin based conditioning with high (200 mg/kg) and low (60 mg/kg) dose cyclophosphamide as upfront treatment in newly diagnosed pediatric patients with acquired SAA incorporating alternative donor sources, including cord blood. Average risk for non‐engraftment patients with <10 transfusions received low dose cyclophosphamide (60 mg/kg); High Risk, those with ≥10 transfusions received conditioning regimen with higher intensity cyclophosphamide (200 mg/kg).ResultsSeventeen patients were enrolled and underwent AlloHSCT including 12 males and 5 females with mean age of 8 years (range 3–16), and median follow‐up time of 39 months (range 1–135). Donor sources included MRD BM (6/6 [n = 9], 5/6 [n = 2]) and unrelated CB (5/6 [n = 4], 4/6 [n = 2]). Five year OS was 67.6% (37.9–85.4). Three secondary graft failures (17.6%) occurred in the low dose cyclophosphamide arm.ConclusionsUpfront treatment with risk‐adapted cyclophosphamide conditioning AlloSCT is well tolerated for the management of newly diagnosed pediatric and adolescent patients with acquired SAA. However, the increased risk of graft rejection in the lower dose arm warrants additional research regarding the optimal intensity of cyclophosphamide‐based conditioning regimen to reduce toxicity without increasing graft failure. Pediatr Blood Cancer 2014;61:1289–1294. © 2014 Wiley Periodicals, Inc.
Clinical features and early treatment response of central nervous system involvement in childhood acute lymphoblastic leukemia
Authors: Levinsen Mette , Taskinen Mervi , Abrahamsson Jonas , Forestier Erik , Frandsen Thomas L. , Harila‐Saari Arja , Heyman Mats , Jonsson Olafur G. , Lähteenmäki Päivi M. , Lausen Birgitte , Vaitkevičienė Goda , Åsberg Ann , Schmiegelow Kjeld ,   on behalf of the Nordic Society of Paediatric Haematology and Oncology (NOPHO)
Published: February 2014

BackgroundCentral nervous system (CNS) involvement in childhood acute lymphoblastic leukemia (ALL) remains a therapeutic challenge.ProcedureTo explore leukemia characteristics of patients with CNS involvement at ALL diagnosis, we analyzed clinical features and early treatment response of 744 patients on Nordic‐Baltic trials. CNS status was classified as CNS1 (no CSF blasts), CNS2 (<5 leukocytes/µl CSF with blasts), CNS3 (≥5 leukocytes/µl with blasts or signs of CNS involvement), TLP+ (traumatic lumbar puncture with blasts), and TLP− (TLP with no blasts).ResultsPatients with CNS involvement had higher leukocyte count compared with patients with CNS1 (P < 0.002). Patients with CNS3 more often had T‐ALL (P < 0.001) and t(9;22)(q34;q11)[BCR‐ABL1] (P < 0.004) compared with patients with CNS1. Among patients with CNS involvement headache (17%) and vomiting (14%) were most common symptoms. Symptoms or clinical findings were present among 27 of 54 patients with CNS3 versus only 7 of 39 patients with CNS2 and 15 of 75 patients with TLP+ (P < 0.001). The majority of patients with CNS involvement received additional induction therapy. The post induction bone marrow residual disease level did not differ between patients with CNS involvement and patients with CNS1 (P > 0.15). The 12‐year event‐free survival for patients with leukemic mass on neuroimaging did not differ from patients with negative or no scan (0.50 vs. 0.60; P = 0.7) or between patients with symptoms or signs suggestive of CNS leukemia and patients without such characteristics (0.50 vs. 0.61; P = 0.2).ConclusionCNS involvement at diagnosis is associated with adverse prognostic features but does not indicate a less chemosensitive leukemia. Pediatr Blood Cancer 2014; 61:1416–1421. © 2014 Wiley Periodicals, Inc.
Terpolymerization kinetics of amino acid N‐carboxy anhydrides
Authors: Zelzer Mischa , Heise Andreas 
Published: February 2014

ABSTRACTBased on their versatility with respect to amino acid type and sequence, polypeptides have become attractive for a number of biological applications such as drug delivery, biomineralization, and drugs. N‐carboxy anhydride (NCA) polymerization is a convenient way to rapidly prepare high‐molecular weight polypeptides with good control over molecular weight and polydispersity. However, the kinetics of the incorporation of NCA monomers into copolypeptides during random copolymerization are poorly understood. Here, kinetic data is presented that allows insight into the NCA polymerization of a terpolymer composed of three commercially relevant amino acids, namely, glutamic acid, lysine, and tyrosine. Furthermore, kinetic data and copolymerization parameters from the copolymerization of binary mixtures of these three amino acid NCAs is used to make predictions of the terpolymer composition. This study provides access to the information necessary to prepare functional copolypeptides with better‐defined sequence architecture that will be essential for the future development of polypeptide‐based materials. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 1228–1236
Patient and health professional's perceived barriers to the delivery of psychosocial care to adults with cancer: a systematic review
Authors: Dilworth Sophie , Higgins Isabel , Parker Vicki , Kelly Brian , Turner Jane 
Published: February 2014

AbstractObjectiveTo explore the barriers experienced and perceived by health professionals and patients in the delivery of psychosocial care to adults with cancer.MethodsSystematic searches were undertaken using the PsychInfo, Medline and CINAHL electronic databases, up to October 2013. Research reporting health professional or patient experiences and perceptions of barriers to psychosocial care are included in the review. The systematic review includes studies that have non‐experimental, exploratory and observational designs, as is appropriate to answer the review question. Included studies were critically appraised. The results of individual quantitative studies were aggregated. Qualitative content analysis was used to analyse the qualitative results.ResultsTwenty‐five papers met the pre‐specified inclusion criteria for the final review. The most commonly perceived barrier for patients relates to receiving adequate support from elsewhere and a lack of perceived need for psychosocial care. Health professionals report barriers at an organisational level most frequently followed by cultural and then individual clinician‐related barriers.ConclusionsBarriers exist on a variety of levels. People with cancer need clear appropriate information and communication about psychosocial services, including information about the role of psychosocial care in addition to existing supports. Interventions that target the complex interplay of individual, organisational and cultural factors need to be developed. Strategies that improve health professional communication skills, identify clear referral pathways, improve acceptability of interventions and clearly identify the need for services could address many of the barriers identified in this review. Copyright © 2014 John Wiley & Sons, Ltd.
Tracking CF disease progression with CT and respiratory symptoms in a cohort of children aged 6–19 years
Authors: Tepper Leonie A. , Caudri Daan , Utens Elisabeth M.W.J. , van der Wiel Els C. , Quittner Alexandra L. , Tiddens Harm A.W.M. 
Published: February 2014

SummaryIntroductionCystic fibrosis (CF) lung disease is characterized by bronchiectasis and trapped air on chest computed tomography (CT).ObjectiveWe aim to validate bronchiectasis and trapped air as outcome measures by evaluating associations between changes in bronchiectasis, trapped air and patient‐reported respiratory symptoms.MethodsA longitudinal cohort study has been conducted. CF patients (aged 6–19 years) who had two routine CTs and completed twice a Cystic Fibrosis Questionnaire‐Revised within 2 years (referred to as T1 and T2), in the period of July 2007 to January 2012 were included. Bronchiectasis and trapped air were scored using the CF‐CT scoring system. Correlation coefficients and student's paired t tests were performed.ResultsIn total 40 patients were included with a median age at T1 of 12.6 years (range 6–17 years), and at T2 14.5 years (range 8–19 years). At T1, bronchiectasis (r = −0.49, P < 0.01) and trapped air (r = −0.34, P = 0.04) correlated with CFQ‐R Respiratory Symptoms Scores (CFQ‐R RSS). At T2 similar correlations were found with the CFQ‐R RSS. Over 2 years, there was significant progression in bronchiectasis (P = 0.03) and trapped air (P = 0.03), but not in CFQ‐R RSS. Changes in bronchiectasis and trapped air were not associated with changes in CFQ‐R RSS.ConclusionOur results indicate that bronchiectasis and trapped are sensitive outcome measures in CF lung disease, showing a significant association with CFQ‐R RSS at two‐time points. However, progression of bronchiectasis and trapped air over 2 year does not necessarily correlate to changes in quality of life. Pediatr Pulmonol. 2014; 49:1182–1189. © 2014 Wiley Periodicals, Inc.
Influence of hydrophobic and electrostatic residues on SARS‐coronavirus S2 protein stability: Insights into mechanisms of general viral fusion and inhibitor design
Authors: Aydin Halil , Al‐Khooly Dina , Lee Jeffrey E. 
Published: February 2014

AbstractSevere acute respiratory syndrome (SARS) is an acute respiratory disease caused by the SARS‐coronavirus (SARS‐CoV). SARS‐CoV entry is facilitated by the spike protein (S), which consists of an N‐terminal domain (S1) responsible for cellular attachment and a C‐terminal domain (S2) that mediates viral and host cell membrane fusion. The SARS‐CoV S2 is a potential drug target, as peptidomimetics against S2 act as potent fusion inhibitors. In this study, site‐directed mutagenesis and thermal stability experiments on electrostatic, hydrophobic, and polar residues to dissect their roles in stabilizing the S2 postfusion conformation was performed. It was shown that unlike the pH‐independent retroviral fusion proteins, SARS‐CoV S2 is stable over a wide pH range, supporting its ability to fuse at both the plasma membrane and endosome. A comprehensive SARS‐CoV S2 analysis showed that specific hydrophobic positions at the C‐terminal end of the HR2, rather than electrostatics are critical for fusion protein stabilization. Disruption of the conserved C‐terminal hydrophobic residues destabilized the fusion core and reduced the melting temperature by 30°C. The importance of the C‐terminal hydrophobic residues led us to identify a 42‐residue substructure on the central core that is structurally conserved in all existing CoV S2 fusion proteins (root mean squared deviation = 0.4 Å). This is the first study to identify such a conserved substructure and likely represents a common foundation to facilitate viral fusion. We have discussed the role of key residues in the design of fusion inhibitors and the potential of the substructure as a general target for the development of novel therapeutics against CoV infections.
CD44 variant 6 is associated with prostate cancer metastasis and chemo‐/radioresistance
Authors: Ni Jie , Cozzi Paul J. , Hao Jing L. , Beretov Julia , Chang Lei , Duan Wei , Shigdar Sarah , Delprado Warick J. , Graham Peter H. , Bucci Joseph , Kearsley John H. , Li Yong 
Published: February 2014

INTRODUCTIONProstate cancer (CaP) is the second leading malignancy in older men in Western countries. The role of CD44 variant 6 (CD44v6) in CaP progression and therapeutic resistance is still uncertain. Here, we investigated the roles of CD44v6 in CaP metastasis and chemo/radioresistance. Expression of CD44v6 in metastatic CaP cell lines, human primary CaP tissues and lymph node metastases was assessed using immunofluorescence and immunohistochemistry, respectively.METHODSKnock down (KD) of CD44v6 was performed in PC‐3M, DU145, and LNCaP cells using small interfering RNA (siRNA), and confirmed by confocal microscope, Western blot and quantitative real time polymerase chain reaction (qRT‐PCR). Cell growth was evaluated by proliferation and colony formation assays. The adhesive ability and invasive potential were assessed using a hyaluronic acid (HA) adhesion and a matrigel chamber assay, respectively. Tumorigenesis potential and chemo‐/radiosensitivity were measured by a sphere formation assay and a colony assay, respectively.RESULTSOver‐expression of CD44v6 was found in primary CaP tissues and lymph node metastases including cancer cells and surrounding stromal cells. KD of CD44v6 suppressed CaP proliferative, invasive and adhesive abilities, reduced sphere formation, enhanced chemo‐/radiosensitivity, and down‐regulated epithelial–mesenchymal transition (EMT), PI3K/Akt/mTOR, and Wnt/β‐catenin signaling pathway proteins in vitro.CONCLUSIONSOur findings demonstrate that CD44v6 is an important cancer stem cell‐like marker associated with CaP proliferation, invasion, adhesion, metastasis, chemo‐/radioresistance, and the induction of EMT as well as the activation PI3K/Akt/mTOR and Wnt signaling pathways, suggesting that CD44v6 is a novel therapeutic target to sensitize CaP cells to chemo/radiotherapy. Prostate 74:602–617, 2014. © 2014 Wiley Periodicals, Inc.
Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization
Authors: Weitzner Brian D. , Kuroda Daisuke , Marze Nicholas , Xu Jianqing , Gray Jeffrey J. 
Published: February 2014

ABSTRACTAntibody Modeling Assessment II (AMA‐II) provided an opportunity to benchmark RosettaAntibody on a set of 11 unpublished antibody structures. RosettaAntibody produced accurate, physically realistic models, with all framework regions and 42 of the 55 non‐H3 CDR loops predicted to under an Ångström. The performance is notable when modeling H3 on a homology framework, where RosettaAntibody produced the best model among all participants for four of the 11 targets, two of which were predicted with sub‐Ångström accuracy. To improve RosettaAntibody, we pursued the causes of model errors. The most common limitation was template unavailability, underscoring the need for more antibody structures and/or better de novo loop methods. In some cases, better templates could have been found by considering residues outside of the CDRs. De novo CDR H3 modeling remains challenging at long loop lengths, but constraining the C‐terminal end of H3 to a kinked conformation allows near‐native conformations to be sampled more frequently. We also found that incorrect VL–VH orientations caused models with low H3 RMSDs to score poorly, suggesting that correct VL–VH orientations will improve discrimination between near‐native and incorrect conformations. These observations will guide the future development of RosettaAntibody. Proteins 2014; 82:1611–1623. © 2014 Wiley Periodicals, Inc.
Selective effects of a therapeutic protein targeting tumor necrosis factor‐alpha on cytochrome P450 regulation during infectious colitis: implications for disease‐dependent drug–drug interactions
Authors: Nyagode Beatrice A. , Jahangardi Roya , Merrell Matthew D. , Tansey Malú G. , Morgan Edward T. 
Published: February 2014

AbstractWe studied the impact of administering XPro1595, a novel antagonist of soluble tumor necrosis factor‐α(TNFα), on the regulation of hepatic cytochrome P450 enzymes in the Citrobacter rodentium model of infectious colitis. XPro1595 was administered subcutaneously every 3 days throughout the infection, or as a single injection near the peak of infection. When given throughout the infection, XPro1595 selectively blocked the downregulation of Cyp3a11 and 3a25 mRNAs, as well as the induction of Cyp2a4/5, without affecting the downregulation of Cyp4a10, Cyp4a14, Cyp2b10, or flavin‐mooxygenase‐3. Induction of Cyp3a11, Cyp3a25, Cyp2c29, and Cyp3a13 mRNAs were observed only in XPro1595‐treated mice. Administration of a single dose of XPro1595 was relatively ineffective. These results (1) confirm the role of soluble TNFα in hepatic Cyp3a regulation during infectious colitis deduced from studies in TNFα receptor‐1 knockout mice; (2) indicate the potential for soluble TNFα ‐specific antagonists to cause disease‐dependent drug–drug interactions; and (3) suggest a novel mechanism by which an anti‐inflammatory therapeutic protein can produce an opposite effect to that of the disease by selectively neutralizing one of multiple signals regulating drug‐metabolizing enzyme expression. More research is needed to determine whether or not this is applicable to other diseases or disease models.
Lessons learned from fire in air supply ducts
Authors: Waller Al , Brown Michelle 
Published: February 2014

In 2012, loss of air flow caused activation of interlocks to shut off steam and electrical heat inputs to an air heating system that was part of a drying/milling operation. Shortly thereafter, upstream filters and air ducts ignited causing more than US$500K in damage and business interruption. Investigations concluded that the interlocks functioned as designed on loss‐of‐airflow but were not sufficient to prevent overheating the inlet air filters (including HEPA filters) by the residual heat in the air heaters. The two main lessons learned from this fire incident apply to a broad range of operations in the chemical process industries (CPI):

Mundane unit operations such as air filters that have combustible components must be evaluated as thoroughly as the rest of the chemical process.
Designers and PHA leaders must recognize the potential of thermal inertia of heaters (and coolers) to heat (or cool) a stagnant volume of fluid when flow is interrupted. Gas streams are particularly susceptible due to the low heat capacity relative to the heat capacity of a metallic heat exchanger. Interlocking the supplies (to steam and electrical heaters in this incident) is often necessary but may not be sufficient.
Other lessons “relearned” include the importance of learning from a previous near miss, the importance of limiting escalation aspects of this fire, and the importance of preventative maintenance. © 2014 American Institute of Chemical Engineers Process Saf Prog, 2014