bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resistance Analyses of Japanese Hepatitis C‐Infected Patients Receiving Sofosbuvir or Ledipasvir/Sofosbuvir Containing Regimens in Phase 3 Studies
Authors: Mizokami M. , Dvory‐Sobol H. , Izumi N. , Nishiguchi S. , Doehle B. , Svarovskaia E. S. , De‐Oertel S. , Knox S. , Brainard D. M. , Miller M. D. , Mo H. , Sakamoto N. , Takehara T. , Omata M. 
Published: May 2016

SummaryHigh rates of sustained virologic response (SVR) has been achieved in Japanese patients with chronic hepatitis C virus (HCV) genotype (GT)1 and GT2 infection treated with ledipasvir/sofosbuvir (LDV/SOF) ±ribavirin (RBV) and SOF+RBV, respectively. We evaluated the effect of baseline HCV NS5A and NS5B resistance‐associated variants (RAVs) on treatment outcome and characterized variants at virologic failure.Baseline deep sequencing for NS5A and NS5B genes was performed for all GT1 patients. Deep sequencing of NS5A (GT1 only) and NS5B (GT1 and GT2) was performed for patients who failed treatment or discontinued early with detectable HCV RNA (i.e., >25 IU/mL). In patients with HCV GT1 infection, 22.3% (GT1a: 2/11; GT1b: 74/330) had ≥1 baseline NS5A RAV. The most frequent NS5A RAVs in GT1b were Y93H (17.9%, 59/330) and L31M (2.4%, 8/330). Despite the presence of NS5A RAVs at baseline, 100% and 97% of patients achieved SVR12, compared with 100% and 99% for those with no NS5A RAVs with LDV/SOF and LDV/SOF+RBV, respectively. All patients with NS5B RAVs at baseline achieved SVR12. Of the 153 patients with GT2 infection (GT2a 60.1%, GT2b 39.9%), 3.3% (5/153) experienced viral relapse. No S282T or other NS5B RAVs were detected at baseline or relapse; no change in susceptibility to SOF or RBV was observed at relapse. In conclusion, LDV/SOF and SOF+RBV demonstrate a high barrier to resistance in Japanese patients with HCV GT1 and GT2 infection. The presence of baseline NS5A RAVs did not impact treatment outcome in GT1 Japanese patients treated with LDV/SOF for 12 weeks.
Rethinking policy perspectives on childhood stunting: time to formulate a structural and multifactorial strategy
Authors: Subramanian S V , Mejía‐Guevara Iván , Krishna Aditi 
Published: May 2016

AbstractStunting and chronic undernutrition among children in South Asia remain a major unresolved global health issue. There are compelling intrinsic and moral reasons to ensure that children attain their optimal growth potential facilitated via promotion of healthy living conditions. Investments in efforts to ensure that children's growth is not faltered also have substantial instrumental benefits in terms of cognitive and economic development. Using the case of India, we critique three prevailing approaches to reducing undernutrition among children: an over‐reliance on macroeconomic growth as a potent policy instrument, a disproportionate focus on interpreting undernutrition as a demand‐side problem and an over‐reliance on unintegrated single‐factorial (one at a time) approaches to policy and research. Using existing evidence, we develop a case for support‐led policy approach with a focus on integrated and structural factors to addressing the problem of undernutrition among children in India.
Key messages

Eliminating child undernutrition is important from an intrinsic perspective and offers considerable instrumental benefits to individual and society.
Evidence suggests that an exclusive reliance on a growth‐mediated strategy to eliminate stunting needs to be reconsidered, suggesting the need for a substantial support‐led strategy.
Interpreting and addressing undernutrition as a demand‐side problem with proximal single‐factorial interventions is futile.
There is an urgent need to develop interventions that address the broader structural and upstream causes of child undernutrition.
Determinants of stunting and poor linear growth in children under 2 years of age in India: an in‐depth analysis of Maharashtra's comprehensive nutrition survey
Authors: Aguayo Víctor M. , Nair Rajilakshmi , Badgaiyan Nina , Krishna Vandana 
Published: May 2016

AbstractWe use a representative sample of 2561 children 0–23 months old to identify the factors most significantly associated with child stunting in the state of Maharashtra, India. We find that 22.7% of children were stunted, with one‐third (7.4%) of the stunted children severely stunted. Multivariate regression analyses indicate that children born with low birthweight had a 2.5‐fold higher odds of being stunted [odds ratio (OR) 2.49; 95% confidence interval (CI) 1.96–3.27]; children 6–23 months old who were not fed a minimum number of times/day had a 63% higher odds of being stunted (OR 1.63; 95% CI 1.24–2.14); and lower consumption of eggs was associated with a two‐fold increased odds of stunting in children 6–23 months old (OR 2.07; 95% CI 1.19–3.61); children whose mother's height was < 145 cm, had two‐fold higher odds of being stunted (OR 2.04; 95% CI 1.46–2.81); lastly, children of households without access to improved sanitation had 88% higher odds of being severely stunted (OR 1.88; 95% CI 1.17–3.02). Attained linear growth (height‐for‐age z‐score) was significantly lower in children from households without access to improved sanitation, children of mothers without access to electronic media, without decision making power regarding food or whose height was < 145 cm, children born with a low birthweight and children 6–23 months old who were not fed dairy products, fruits and vegetables. In Maharashtra children's birthweight and feeding practices, women's nutrition and status and household sanitation and poverty are the most significant predictors of stunting and poor linear growth in children under 2 years.
Key messages

One in five (22.7%) of children 0–23 months old in the state of Maharashtra were stunted, and one‐third (7.4%) of the stunted children were severely stunted.
Birthweight, child feeding, women's nutrition and household sanitation were the most significant predictors of stunting and poor linear growth in children under 2 years.
Children born to mothers whose height was below 145 cm, had two‐fold higher odds of being stunted; children born with a low birthweight had a 2.5‐fold higher odds of being stunted.
Low feeding frequency and low consumption of eggs, dairy products, fruits and vegetables were associated with stunting and poor linear growth in children 6–23 months old.
Children of households without access to improved sanitation had 88% higher odds of being severely stunted.
The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene
Authors: Chowdhury Chiranjit , Chun Sunny , Sawaya Michael R. , Yeates Todd O. , Bobik Thomas A 
Published: May 2016

SummaryBacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2‐propanediol (1,2‐PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2‐PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2‐PD transport. The crystal structure revealed that PduJ was nearly identical to that of PduA and, hence, offered no explanation for their differential functions. Interestingly, however, when a pduJ gene was placed at the pduA chromosomal locus, the PduJ protein acquired a new function, the ability to mediate 1,2‐PD transport into the Pdu MCP. To our knowledge, these are the first studies to show that that gene location can determine the function of a MCP shell protein. We propose that gene location dictates protein‐protein interactions essential to the function of the MCP shell.
A Crisis of Ends: University Education as Formative Reading
Authors: Lorkovic Edvard 
Published: May 2016

AbstractBeginning with Mark C. Taylor's Crisis on Campus, and its critique of the structure and delivery of contemporary higher education, this essay argues that if there is a crisis in education, it is not technical, not reducible to the delivery of education. If there is a crisis, it lies in the contemporary world's misunderstanding of the goals or ends of the university. Borrowing Antonin's Sertillanges’ account of reading from the Intellectual Life, the essay concludes by suggesting that the goal of university education is formation of the mind, not mastery, edification, of entertainment.
François Pourfour du Petit (1664–1741): pioneer in ocular biometry
Authors: Charman W Neil 
Published: May 2016

AbstractPurposeTo outline the important contributions of the French physician Petit to the development of ocular biometry.ContentAfter a brief review of Petit's life and his studies in neurology, anatomy, and cataract surgery, the methodology and results of his work in measuring many of the biometric parameters of the human eye are discussed. Among other techniques, he made use of frozen sections of eyes to explore their dimensions and employed an immersion technique to avoid the effect of corneal refraction on the appearance of the iris. His pioneering biometric results have been largely confirmed by modern studies. Those on the changes in the crystalline lens with age are particularly striking and suggest that these ocular aging effects have changed little over the last 300 years. Although largely forgotten today, his biometric work exercised a considerable influence on his more immediate successors, including Porterfield and Thomas Young.SummaryFrançois Pourfour du Petit deserves to be remembered as an important contributor to our understanding of the structure and dimensions of the human eye.
A Mechanics Model for Sensors Imperfectly Bonded to the Skin for
Determination of the Young's Moduli of Epidermis and Dermis
Authors: Yuan J. H. , Shi Y. , Pharr M. , Feng X. , Rogers John A. , Huang Yonggang 
Published: May 2016

Abstract
A mechanics model is developed for the encapsulated piezoelectric thin-film actuators/sensors system imperfectly bonded to the human skin to simultaneously determine the Young's moduli of the epidermis and dermis as well as the thickness of epidermis.
ACOUSTICAL STANDARDS NEWS
Authors: Blaeser Susan B. , Struck Christopher J. 
Published: May 2016

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, S3/SC 1, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, animal bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA).
Comments are welcomed on all material in Acoustical Standards News.
This Acoustical Standards News section in JASA, as well as the national catalog of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Pore chemistry and size control in hybrid porous materials for acetylene capture from ethylene
Authors: Cui Xili , Chen Kaijie , Xing Huabin , Yang Qiwei , Krishna Rajamani , Bao Zongbi , Wu Hui , Zhou Wei , Dong Xinglong , Han Yu , Li Bin , Ren Qilong , Zaworotko Michael J. , Chen Banglin 
Published: May 2016

Separating one organic from another
Separating closely related organic molecules is a challenge (see the Perspective by Lin).The separation of acetylene from ethylene is needed in high-purity polymer production. Cui et al. developed a copper-based metal-organic framework with hexafluorosilicate and organic linkers designed to have a high affinity for acetylene. These materials, which capture four acetylene molecules in each pore, successfully separated acetylene from mixtures with ethylene. Propane and propylene are both important feedstock chemicals. Their physical and chemical similarity, however, requires energy-intense processes to separate them. Cadiau et al. designed a fluorinated porous metal-organic framework material that selectively adsorbed propylene, with the complete exclusion of propane.

Science
, this issue pp.
141
and
137
; see also p.
121
Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women
Authors: Mandal Paramita , Bhattacharjee Bornali , Sen Shrinka , Bhattacharya Amrapali , Roy Chowdhury Rahul , Mondal Nidhu Ranjan , Sengupta Sharmila 
Published: May 2016

ABSTRACT

Human papillomavirus type 16 (HPV16), a member of the
Papillomaviridae
family, is the primary etiological agent of cervical cancer. Here, we report the complete genome sequences of four HPV16 Asian American variants and four European variants, isolated from cervical biopsies and scrapings in India.
The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production
Authors: Aleti Gajender , Antonielli Livio , Corretto Erika , Nikolić Branislav , Sessitsch Angela , Brader Günter 
Published: May 2016

ABSTRACT

We report here the draft genome sequence of
Paenibacillus polymyxa
strain CCI-25, which displays strong antifungal and antibacterial activities
in vitro
. The genome encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin, polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to paenicidin A, as well as a type 1 polyketide synthase.
Genome Sequence of
Enterococcus pernyi
, a Pathogenic Bacterium for the Chinese Oak Silkworm,
Antheraea pernyi
Authors: Sun Ying , Li Xisheng , Wang Guobao , Wang Yong , Jiang Yiren , Liu Yanqun , Yu Zhiguo , Qin Li 
Published: May 2016

ABSTRACT

We report the draft genome assembly of
Enterococcus pernyi
. The genome sequence is 3.09 Mb in length with a G+C content of 38.35%. It covers 3,153 genes with an average length of 854 bp, and contains 65 tRNAs, 13 small RNAs, and 18 rRNAs. Moreover, it contains 9 genomic islands with an average length of 14,058 bp and 3 prophages with an average length of 37,430 bp.
Lower Pectoralis Muscle Area Is Associated with a Worse Overall Survival in Non–Small Cell Lung Cancer
Authors: Kinsey C. Matthew , San José Estépar Raul , van der Velden Jos , Cole Bernard F. , Christiani David C. , Washko George R. 
Published: May 2016

Abstract
Background: Muscle wasting is a component of the diagnosis of cancer cachexia and has been associated with poor prognosis. However, recommended tools to measure sarcopenia are limited by poor sensitivity or the need to perform additional scans. We hypothesized that pectoralis muscle area (PMA) measured objectively on chest CT scan may be associated with overall survival (OS) in non–small cell lung cancer (NSCLC).
Methods: We evaluated 252 cases from a prospectively enrolling lung cancer cohort. Eligible cases had CT scans performed prior to the initiation of surgery, radiation, or chemotherapy. PMA was measured in a semi-automated fashion while blinded to characteristics of the tumor, lung, and patient outcomes.
Results: Men had a significantly greater PMA than women (37.59 vs. 26.19 cm2, P &lt; 0.0001). In univariate analysis, PMA was associated with age and body mass index (BMI). A Cox proportional hazards model was constructed to account for confounders associated with survival. Lower pectoralis area (per cm2) at diagnosis was associated with an increased hazard of death of 2% (HRadj, 0.98; confidence interval, 0.96–0.99; P = 0.044) while adjusting for age, sex, smoking, chronic bronchitis, emphysema, histology, stage, chemotherapy, radiation, surgery, BMI, and ECOG performance status.
Conclusions: Lower PMA measured from chest CT scans obtained at the time of diagnosis of NSCLC is associated with a worse OS.
Impact: PMA may be a valuable CT biomarker for sarcopenia-associated lung cancer survival. Cancer Epidemiol Biomarkers Prev; 26(1); 38–43. ©2016 AACR.
See all the articles in this CEBP Focus section, “The Obesity Paradox in Cancer: Evidence and New Directions.”
Alcohol Use and Breast Cancer Survival among Participants in the Women's Health Initiative
Authors: Lowry Sarah J. , Kapphahn Kris , Chlebowski Rowan , Li Christopher I. 
Published: May 2016

Abstract
Background: Alcohol increases the risk of breast cancer even at moderate levels of intake. However, the relationship between alcohol consumption and mortality among breast cancer patients is less clear.
Methods: This study included women from the Women's Health Initiative observational study and randomized trial diagnosed with breast cancer (n = 7,835). Cox proportional hazards regression was used to estimate adjusted HRs and 95% confidence intervals (CI) for overall and breast cancer–specific (BCS) mortality associated with drinking alcohol before or after a breast cancer diagnosis. We also assessed whether changes in drinking habits after diagnosis are related to mortality.
Results: Women who were consuming alcohol prior to their breast cancer diagnosis had a nonstatistically significant 24% (95% CI, 0.56–1.04) reduced risk of BCS mortality and a 26% (95% CI, 0.61–0.89) reduced risk of all-cause mortality. Some variation was observed by estrogen receptor (ER) status as alcohol consumption was associated with a 49% (95% CI, 0.31–0.83) reduced risk of BCS mortality among ER− patients with no change in risk observed among ER+ patients (HR = 0.97; 95% CI, 0.31–1.54), though the difference between these risks was not statistically significant (P for interaction = 0.39). Postdiagnosis alcohol consumption, and change in consumption patterns after diagnosis, did not appear to be associated with all-cause or BCS mortality.
Conclusion: In this large study, consumption of alcohol before or after breast cancer diagnosis did not increase risks of overall or cause-specific mortality.
Impact: Coupled with existing evidence, alcohol consumption is unlikely to have a substantial impact on mortality among breast cancer patients. Cancer Epidemiol Biomarkers Prev; 25(8); 1268–73. ©2016 AACR.
Ultrastructural Insights into the Biological Significance of Persisting DNA Damage Foci after Low Doses of Ionizing Radiation
Authors: Lorat Yvonne , Schanz Stefanie , Rübe Claudia E. 
Published: May 2016

Abstract
Purpose: Intensity-modulated radiotherapy (IMRT) enables the delivery of high doses to target volume while sparing surrounding nontargeted tissues. IMRT treatment, however, substantially increases the normal tissue volume receiving low-dose irradiation, but the biologic consequences are unclear.
Experimental Design: Using mouse strains that varied in genetic DNA repair capacity, we investigated the DNA damage response of cortical neurons during daily low-dose irradiation (0.1 Gy). Using light and electron microscopic approaches, we enumerated and characterized DNA damage foci as marker for double-strand breaks (DSBs).
Results: During repeated low-dose irradiation, cortical neurons in brain tissues of all mouse strains had a significant increase of persisting foci with cumulative doses, with the most pronounced accumulation of large-sized foci in repair-deficient mice. Electron microscopic analysis revealed that persisting foci in repair-proficient neurons reflect chromatin alterations in heterochromatin, but not persistently unrepaired DSBs. Repair-deficient SCID neurons, by contrast, showed high numbers of unrepaired DSBs in eu- and heterochromatin, emphasizing the fundamental role of DNA-PKcs in DSB rejoining, independent of chromatin status. In repair-deficient ATM−/− neurons, large persisting damage foci reflect multiple unrepaired DSBs concentrated at the boundary of heterochromatin due to disturbed KAP1 phosphorylation.
Conclusion: Repeated low-dose irradiation leads to the accumulation of persisting DNA damage foci in cortical neurons and thus may adversely affect brain tissue and increase the risk of carcinogenesis. Multiple unrepaired DSBs account for large-sized foci in repair-deficient neurons, thus quantifying foci alone may underestimate extent and complexity of persistent DNA damage. Clin Cancer Res; 22(21); 5300–11. ©2016 AACR.
The Obama Administration's Cancer Moonshot: A Call for Proteomics
Authors: Conrads Thomas P. , Petricoin Emanuel F. 
Published: May 2016

Abstract
The Cancer Moonshot Program has been launched and represents a potentially paradigm-shifting initiative with the goal to implement a focused national effort to double the rate of progress against cancer. The placement of precision medicine, immunotherapy, genomics, and combination therapies was placed at the central nexus of this initiative. Although we are extremely enthusiastic about the goals of the program, it is time we meet this revolutionary project with equally bold and cutting-edge ideas: it is time we move firmly into the postgenome era and provide the necessary resources to propel and seize on innovative recent gains in the field of proteomics required for it to stand on equal footing in this narrative as a combined, synergistic engine for molecular profiling. After all, although the genome is the information archive, it is the proteins that actually do the work of the cell and represent the structural cellular machinery. It is the proteins that comprise most of the biomarkers that are measured to detect cancers, constitute the antigens that drive immune response and inter- and intracellular communications, and it is the proteins that are the drug targets for nearly every targeted therapy that is being evaluated in cancer trials today. We believe that a combined systems biology view of the tumor microenvironment that orients cancer studies back to the functional proteome, phosphoproteome, and biochemistry of the cell will be essential to deliver on the promise of the Cancer Moonshot Program. Clin Cancer Res; 22(18); 4556–8. ©2016 AACR.