bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directly observed therapy of sofosbuvir/ribavirin +/− peginterferon with minimal monitoring for the treatment of chronic hepatitis C in people with a history of drug use in Chennai, India (C‐DOT)
Authors: Solomon S. S. , Sulkowski M. S. , Amrose P. , Srikrishnan A. K. , McFall A. M. , Ramasamy B. , Kumar M. S. , Anand S. , Thomas D. L. , Mehta S. H. 
Published: July 2017

SummaryWe assessed the feasibility of field‐based directly observed therapy (DOT) with minimal monitoring to deliver HCV treatment to people with a history of drug use in Chennai, India. Fifty participants were randomized 1:1 to sofosbuvir+peginterferon alfa 2a+ribavirin (SOF+PR) for 12 weeks (Arm 1) vs sofosbuvir+ribavirin (SOF+R) for 24 weeks (Arm 2). SOF+R was delivered daily at participant chosen venues and weekly peginterferon injections at the study clinic. HCV RNA testing was performed to confirm active HCV infection and sustained virologic response 12 weeks after treatment completion (SVR12). No baseline genotyping or on‐treatment viral loads were performed. Median age was 46 years. All were male and 20% had significant fibrosis/cirrhosis. All self‐reported history of injection drug use, 18% recent noninjection drug use and 38% alcohol dependence. Six discontinued treatment (88% completed treatment in each arm). Of 22 who completed SOF+PR, all achieved SVR12 (22/25=88%); 15 of 22 who completed SOF+R achieved SVR12 (15/25=60%; P=.05). Among those completing SOF+R, SVR12 was significantly less common in participants reporting ongoing substance use (36% vs 100%) and missed doses. Active substance use and missed doses did not impact SVR with SOF+PR. Field‐based DOT of HCV therapy without real‐time HCV RNA monitoring was feasible; however, achieving 100% adherence was challenging. SOF+PR appeared superior to SOF+R in achieving SVR12, even when doses were missed with no discontinuations due to side effects. Further exploration of short duration treatment with peginterferon plus direct‐acting antivirals is warranted.
Development of iFOX‐hunting as a functional genomic tool and demonstration of its use to identify early senescence‐related genes in the polyploid Brassica napus
Authors: Ling Juan , Li Renjie , Nwafor Chinedu Charles , Cheng Junluo , Li Maoteng , Xu Qing , Wu Jian , Gan Lu , Yang Qingyong , Liu Chao , Chen Ming , Zhou Yongming , Cahoon Edgar B. , Zhang Chunyu 
Published: July 2017

SummaryFunctional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain‐of‐function platform, termed ‘iFOX (inducible Full‐length cDNA OvereXpressor gene)‐Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway‐compatible plant gene expression vector containing a methoxyfenozide‐inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium‐mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and to control developmental timing of transgene expression. Evaluation of a subset of the resulting ~6000 Arabidopsis transformants revealed a high percentage of lines with full‐length B. napus transgene insertions. Upon induction, numerous iFOX lines with visible phenotypes were identified, including one that displayed early leaf senescence. Phenotypic analysis of this line (rsl‐1327) after methoxyfenozide induction indicated high degree of leaf chlorosis. The integrated B. napuscDNA was identified as a homolog of an Arabidopsis acyl‐CoA binding protein (ACBP) gene designated BnACBP1‐like. The early senescence phenotype conferred by BnACBP1‐like was confirmed by constitutive expression of this gene in Arabidopsis and B. napus. Use of the inducible promoter in the iFOX line coupled with RNA‐Seq analyses allowed mechanistic clues and a working model for the phenotype associated with BnACBP1‐like expression. Our results demonstrate the utility of iFOX‐Hunting as a tool for gene discovery and functional characterization of Brassica napus genome.
Virulence determines beneficial trade‐offs in the response of virus‐infected plants to drought via induction of salicylic acid
Authors: Aguilar Emmanuel , Cutrona Carmen , del Toro Francisco J. , Vallarino José G. , Osorio Sonia , Pérez‐Bueno María Luisa , Barón Matilde , Chung Bong‐Nam , Canto Tomás , Tenllado Francisco 
Published: July 2017

AbstractIt has been hypothesized that plants can get beneficial trade‐offs from viral infections when grown under drought conditions. However, experimental support for a positive correlation between virus‐induced drought tolerance and increased host fitness is scarce. We investigated whether increased virulence exhibited by the synergistic interaction involving Potato virus X (PVX) and Plum pox virus (PPV) improves tolerance to drought and host fitness in Nicotiana benthamiana and Arabidopsis thaliana. Infection by the pair PPV/PVX and by PPV expressing the virulence protein P25 of PVX conferred an enhanced drought‐tolerant phenotype compared with single infections with either PPV or PVX. Decreased transpiration rates in virus‐infected plants were correlated with drought tolerance in N. benthamiana but not in Arabidopsis. Metabolite and hormonal profiles of Arabidopsis plants infected with the different viruses showed a range of changes that positively correlated with a greater impact on drought tolerance. Virus infection enhanced drought tolerance in both species by increasing salicylic acid accumulation in an abscisic acid‐independent manner. Viable offspring derived from Arabidopsis plants infected with PPV increased relative to non‐infected plants, when exposed to drought. By contrast, the detrimental effect caused by the more virulent viruses overcame potential benefits associated with increased drought tolerance on host fitness.
Evaluating sermons: The function of grades in teaching preaching
Authors: Helsel Carolyn Browning 
Published: July 2017

AbstractWhat are grades doing in a homiletics classroom? This article traces the function of grades through the broader history of the educational system in the United States and then makes suggestions for how grades can be used more effectively in teaching preaching. Beginning in the nineteenth century, teachers used grades to rank and motivate students, as well as communicate across institutions. With the more recent assessment movement, educators have conceptualized grading as the larger process of evaluating the success of learning objectives. The commission on accreditation for the Association of Theological Schools does not view grades as part of its assessment, but it evaluates theological schools on whether they achieve intended learning outcomes. Theological educators need to be able to evaluate whether their teaching fulfills their schools' mission and learning objectives. For homiletics, the author measures learning through pre‐ and post‐preaching feedback and incorporates professor‐ and student‐crafted rubrics.
Reducing tillage intensity affects the cumulative emergence dynamics of annual grass weeds in winter cereals
Authors: Scherner A , Melander B , Jensen P K , Kudsk P , Avila LA 
Published: July 2017

SummaryAnnual grass weeds such as Apera spica‐venti and Vulpia myuros are promoted in non‐inversion tillage systems and winter cereal‐based crop rotations. Unsatisfactory weed control in these conditions is often associated with a poor understanding of the emergence pattern of these weed species. The aim of this study was to investigate, understand and model the cumulative emergence patterns of A. spica‐venti, V. myuros and Poa annua in winter cereals grown in three primary tillage regimes: (i) mouldboard ploughing, (ii) pre‐sowing tine cultivation to 8–10 cm soil depth and (iii) direct drilling. Direct drilling delayed the cumulative emergence of A. spica‐venti and V. myuros (counted together) in contrast with ploughing, while the emergence pattern of P. annua was unaffected by the type of tillage system. The total density of emerged weed seedlings varied between the tillage systems and years with a higher total emergence seen under direct drilling, followed by pre‐sowing tine cultivation and ploughing. The emergence patterns of all species were differently influenced by the tillage systems, suggesting that under direct drilling, in which these species occur simultaneously, management interventions should first and foremost consider that A. spica‐venti and V. myuros emerge over a longer period to avoid control failures.
Transmission of Resistant Gram-Negative Bacteria to Health Care Worker Gowns and Gloves during Care of Nursing Home Residents in Veterans Affairs Community Living Centers
Authors: Blanco Natalia , Pineles Lisa , Lydecker Alison D. , Johnson J. Kristie , Sorkin John D. , Morgan Daniel J. ,   the VA Gown and Glove Investigators, Roghmann Mary-Claire 
Published: July 2017

ABSTRACTThe objectives of the study were to estimate the risk of transmission of antibiotic-resistant Gram-negative bacteria (RGNB) to gowns and gloves (G&G) worn by health care workers (HCWs) when providing care to nursing home residents and to identify the types of care and resident characteristics associated with transmission. A multicenter, prospective observational study was conducted with residents and HCWs from Veterans Affairs (VA) nursing homes. Perianal swabs to detect RGNB were collected from residents. HCWs wore G&G during usual care activities, and the G&G were swabbed at the end of the interaction in a standardized manner. Transmission of RGNB from a colonized resident to G&G by type of care was measured. Odds ratios (ORs) associated with type of care or resident characteristics were estimated. Fifty-seven (31%) of 185 enrolled residents were colonized with ≥1 RGNB. RGNB transmission to HCW gloves or gowns occurred during 9% of the interactions (n= 905): 7% to only gloves and 2% to only gowns. Bathing the resident and providing hygiene and toilet assistance were associated with a high risk of transmission. Glucose monitoring and assistance with feeding or medication were associated with a low risk of transmission. In addition, antibiotic use by the resident was strongly associated with greater transmission (OR, 2.51;P< 0.01). RGNB were transferred to HCWs during ∼9% of visits. High-risk types of care were identified for which use of G&G may be prioritized. Antibiotic use was associated with 2.5 times greater risk of transmission, emphasizing the importance of antibiotic stewardship. (This study has been registered at ClinicalTrials.gov under registration no. NCT01350479.)
Phagocytic Receptors Activate Syk and Src Signaling during Borrelia burgdorferi Phagocytosis
Authors: Killpack Tess L. , Ballesteros Maria , Bunnell Stephen C. , Bedugnis Alice , Kobzik Lester , Hu Linden T. , Petnicki-Ocwieja Tanja 
Published: July 2017

ABSTRACTPhagocytosis of the Lyme disease-causing pathogenBorrelia burgdorferihas been shown to be important for generating an inflammatory response to the pathogen. As a result, understanding the mechanisms of phagocytosis has been an area of great interest in the field of Lyme disease. Several cell surface receptors that participate inB. burgdorferiphagocytosis have been reported, including the scavenger receptor MARCO and integrin α3β1. We sought to define the mechanisms by which these receptors mediate phagocytosis and to identify signaling pathways activated downstream of these receptors upon contact withB. burgdorferi. We identified both Syk and Src signaling pathways as ones that participate inB. burgdorferiphagocytosis and the resulting cytokine activation. In our studies, we found that both MARCO and integrin β1 play a role in the activation of the Src kinase pathway. However, only integrin β1 participates in the activation of Syk. Interestingly, the integrin activates Syk without the help of the signaling adaptor Dap12 or FcRγ. Thus, we report that multiple pathways participate inB. burgdorferiinternalization and that different cell surface receptors act simultaneously in cooperation and independently to mediate phagocytosis.
Metabolite Transporter PEG344 Is Required for Full Virulence of Hypervirulent Klebsiella pneumoniae Strain hvKP1 after Pulmonary but Not Subcutaneous Challenge
Authors: Bulger Jeffrey , MacDonald Ulrike , Olson Ruth , Beanan Janet , Russo Thomas A. 
Published: July 2017

ABSTRACT

Hypervirulent
Klebsiella pneumoniae
(hvKP) is an emerging pathotype that is capable of causing tissue-invasive and organ- and life-threatening infections in healthy individuals from the community. Knowledge on the virulence factors specific to hvKP is limited. In this report, we describe a new factor (PEG344) that increases the virulence of hvKP strain hvKP1.
peg-344
is present on the hvKP1 virulence plasmid, is broadly prevalent among hvKP strains, and has increased RNA abundance when grown in human ascites. An isogenic derivative of hvKP1 (hvKP1Δ
peg-344
) was constructed and compared with its wild-type parent strain in
in vitro
,
ex vivo
, and infection model studies. Both survival and competition experiments with outbred CD1 mice demonstrated that PEG344 was required for full virulence after pulmonary challenge but, interestingly, not after subcutaneous challenge.
In silico
analysis suggested that PEG344 serves as an inner membrane transporter. Compared to hvKP1, a small but significant decrease in the growth/survival of hvKP1Δ
peg-344
was observed in human ascites, but resistance to the bactericidal activity of complement was similar. These data suggested that PEG344 may transport an unidentified growth factor present in ascites. The data presented are important since they expand our limited knowledge base on virulence factors unique to hvKP, which is needed to lay the groundwork for translational approaches to prevent or treat these devastating infections.
On the origin of nonlocal damping in plasmonic monomers and dimers
Authors: Tserkezis Christos , Yan Wei , Hsieh Wenting , Sun Greg , Khurgin Jacob B. , Wubs Martijn , Mortensen N. Asger 
Published: July 2017

The origin and importance of nonlocal damping is discussed through simulations with the generalized nonlocal optical response (GNOR) theory, in conjunction with time-dependent density functional theory (TDDFT) calculations and equivalent circuit modeling, for some of the most typical plasmonic architectures: metal–dielectric interfaces, metal–dielectric–metal gaps, spherical nanoparticles and nanoparticle dimers. It is shown that diffusive damping, as introduced by the convective–diffusive GNOR theory, describes well the enhanced losses and plasmon broadening predicted by ab initio calculations in few-nm particles or few-to-sub-nm gaps. Through the evaluation of a local effective dielectric function, it is shown that absorptive losses appear dominantly close to the metal surface, in agreement with TDDFT and the mechanism of Landau damping due to generation of electron–hole pairs near the interface. Diffusive nonlocal theories provide therefore an efficient means to tackle plasmon damping when electron tunneling can be safely disregarded, without the need to resort to more accurate, but time-consuming fully quantum-mechanical studies.
Modelling basalt weathering at elevated CO
2
concentrations: implications for terminal to post-magmatic rifting in the Deccan Traps, Kachchh, India
Authors: Mitra Kaushik , Mitra Souvik , Gupta Saibal , Bhattacharya Satadru , Chauhan Prakash , Jain Nirmala 
Published: July 2017

Abstract

Deccan volcanism was synchronous with rifting along the west coast of India. Pre- and synmagmatic rifting has been widely reported in the Deccan Volcanic Province, but extension post-dating magmatism, and predating India–Eurasia collision, is less well known. A recent study in the Kachchh area of western India documented weathering of basalts to kaolinite at the base of Cenozoic rift basins, with rift flanks relatively less altered to smectites, and this was attributed to post-magmatic rifting. This study models basalt weathering under open- and closed-system conditions to simulate rainwater interacting with basalts either on topographical slopes (within rifts) or on flat-topped hills (flow tops). Both systems were modelled under

p

C

O

2

conditions ranging from low, present-day values to higher values more appropriate for the end-Cretaceous–early Paleocene time, after basalt emplacement. The results show that if

p

C

O

2

exceeded values of 10
−2.5
, basalts would be altered to kaolinite in both open and closed systems. Existing

p

C

O

2

estimates in the aftermath of Deccan volcanism fall below this value, implying that the differential basalt weathering was more likely to have been caused by terminal to post-magmatic rifting. This indicates that extensional tectonics along the Indian west coast in the Kachchh region continued even after cessation of Deccan volcanism.
HDAC1 Upregulation by NANOG Promotes Multidrug Resistance and a Stem-like Phenotype in Immune Edited Tumor Cells
Authors: Song Kwon-Ho , Choi Chel Hun , Lee Hyo-Jung , Oh Se Jin , Woo Seon Rang , Hong Soon-Oh , Noh Kyung Hee , Cho Hanbyoul , Chung Eun Joo , Kim Jae-Hoon , Chung Joon-Yong , Hewitt Stephen M. , Baek Seungki , Lee Kyung-Mi , Yee Cassian , Son Minjoo , Mao Chih-Ping , Wu T.C. , Kim Tae Woo 
Published: July 2017

Abstract
Cancer immunoediting drives the adaptation of tumor cells to host immune surveillance. Immunoediting driven by antigen (Ag)-specific T cells enriches NANOG expression in tumor cells, resulting in a stem-like phenotype and immune resistance. Here, we identify HDAC1 as a key mediator of the NANOG-associated phenotype. NANOG upregulated HDAC1 through promoter occupancy, thereby decreasing histone H3 acetylation on K14 and K27. NANOG-dependent, HDAC1-driven epigenetic silencing of cell-cycle inhibitors CDKN2D and CDKN1B induced stem-like features. Silencing of TRIM17 and NOXA induced immune and drug resistance in tumor cells by increasing antiapoptotic MCL1. Importantly, HDAC inhibition synergized with Ag-specific adoptive T-cell therapy to control immune refractory cancers. Our results reveal that NANOG influences the epigenetic state of tumor cells via HDAC1, and they encourage a rational application of epigenetic modulators and immunotherapy in treatment of NANOG+ refractory cancer types. Cancer Res; 77(18); 5039–53. ©2017 AACR.
Prediction of Clinical Outcome After Acute Ischemic Stroke
Authors: Dankbaar Jan W. , Horsch Alexander D. , van den Hoven Andor F. , Kappelle L. Jaap , van der Schaaf Irene C. , van Seeters Tom , Velthuis Birgitta K. 
Published: July 2017

Background and Purpose—
Early prediction of outcome in acute ischemic stroke is important for clinical management. This study aimed to compare the relationship between early follow-up multimodality computed tomographic (CT) imaging and clinical outcome at 90 days in a large multicenter stroke study.

Methods—
From the DUST study (Dutch Acute Stroke Study), patients were selected with (1) anterior circulation occlusion on CT angiography (CTA) and ischemic deficit on CT perfusion (CTP) on admission, and (2) day 3 follow-up noncontrast CT, CTP, and CTA. Follow-up infarct volume on noncontrast CT, poor recanalization on CTA, and poor reperfusion on CTP (mean transit time index ≤75%) were related to unfavorable outcome after 90 days defined as modified Rankin Scale 3 to 6. Four multivariable models were constructed: (1) only baseline variables (model 1), (2) model 1 with addition of infarct volume, (3) model 1 with addition of recanalization, and (4) model 1 with addition of reperfusion. Area under the curves of the receiver operating characteristic curves of the models were compared using the DeLong test.

Results—

A total of 242 patients were included. Poor recanalization was found in 21%, poor reperfusion in 37%, and unfavorable outcome in 44%. The area under the curve of the receiver operating characteristic curve without follow-up imaging was 0.81, with follow-up noncontrast CT 0.85 (
P
=0.02), CTA 0.86 (
P
=0.01), and CTP 0.86 (
P
=0.01). All 3 follow-up imaging modalities improved outcome prediction compared with no imaging. There was no difference between the imaging models.

Conclusions—
Follow-up imaging after 3 days improves outcome prediction compared with prediction based on baseline variables alone. CTA recanalization and CTP reperfusion do not outperform noncontrast CT at this time point.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00880113.
Puccinellia poecilantha (Poaceae) in Iran
Authors: NAQINEZHAD ALIREZA , HAMEDANI HAJAR 
Published: July 2017

Puccinellia is one of the most taxonomically difficult grass genera in the Poeae tribe. The genus is represented by ten species in Iran confined mainly to saline habitats. Based on new collections from northeast Iran, we verify P. poecilantha as occurring in Iran. The specimen identified as P. poecilantha in the Flora Iranica was misidentified, and is corrected to P. gigantea. Puccinellia poecilantha differs from P. bulbosa and P. gigantea, the two most morphologically similar species in Iran, by shape and sizes of their lemmas and glumes, and indumentum. Anatomical features of P. poecilantha are discussed and a distribution map for the new record is provided.
Internally Generated and Externally Forced Multidecadal Oceanic Modes and Their Influence on the Summer Rainfall over East Asia
Authors: Si Dong , Hu Aixue 
Published: July 2017

Abstract
Interdecadal oceanic variabilities can be generated from both internal and external processes, and these variabilities can significantly modulate climate on global and regional scales, including the warming slowdown in the early twenty-first century and rainfall in East Asia. By analyzing simulations from a unique Community Earth System Model (CESM) Large Ensemble (CESM-LE) project, it is shown that the interdecadal Pacific oscillation (IPO) is primarily an internally generated oceanic variability, while the Atlantic multidecadal oscillation (AMO) may be an oceanic variability generated by internal oceanic processes and modulated by external forcing in the twentieth century. Although the observed relationship between IPO and the Yangtze–Huaihe River valley (YHRV) summer rainfall in China is well simulated in both the preindustrial control and the twentieth-century ensemble simulation, none of the twentieth-century ensemble members can reproduce the observed time evolution of both the IPO and YHRV rainfall because of the unpredictable nature of IPO on multidecadal time scales. On the other hand, although CESM-LE cannot reproduce the observed relationship between the AMO and Huanghe River valley (HRV) summer rainfall of China in the preindustrial control simulation, this relationship in the twentieth-century simulations is well reproduced, and the chance of reproducing the observed time evolution of both AMO and HRV rainfall is about 30%, indicating the important role of the interaction between the internal processes and the external forcing to realistically simulate the AMO and HRV rainfall.