bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013
Authors: du Plessis Mignon , Allam Mushal , Tempia Stefano , Wolter Nicole , de Gouveia Linda , von Mollendorf Claire , Jolley Keith A. , Mbelle Nontombi , Wadula Jeannette , Cornick Jennifer E. , Everett Dean B. , McGee Lesley , Breiman Robert F. , Gladstone Rebecca A. , Bentley Stephen D. , Klugman Keith P. , von Gottberg Anne 
Published: March 2016

ABSTRACT

Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following the introduction of the 13-valent pneumococcal conjugate vaccine in 2011. We genetically characterized 912 invasive serotype 1 isolates from 1989 to 2013. Simpson's diversity index (D) and recombination ratios were calculated. Factors associated with sequence types (STs) were assessed. Clonal complex 217 represented 96% (872/912) of the sampled isolates. Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), ST diversity increased in children <5 years (D, 0.39 to 0.63,
P
= 0.002) and individuals >14 years (D, 0.35 to 0.54,
P
< 0.001): ST-217 declined proportionately in children <5 years (153/203 [75%] versus 21/37 [57%],
P
= 0.027) and individuals >14 years (242/305 [79%] versus 96/148 [65%],
P
= 0.001), whereas ST-9067 increased (4/684 [0.6%] versus 24/228 [11%],
P
< 0.001). Three subclades were identified within ST-217: ST-217
C1
(353/382 [92%]), ST-217
C2
(15/382 [4%]), and ST-217
C3
(14/382 [4%]). ST-217
C2
, ST-217
C3
, and single-locus variant (SLV) ST-8314 (20/912 [2%]) were associated with nonsusceptibility to chloramphenicol, tetracycline, and co-trimoxazole. ST-8314 (20/912 [2%]) was also associated with increased nonsusceptibility to penicillin (
P
< 0.001). ST-217
C3
and newly reported ST-9067 had higher recombination ratios than those of ST-217
C1
(4.344 versus 0.091,
P
< 0.001; and 0.086 versus 0.013,
P
< 0.001, respectively). Increases in genetic diversity were noted post-PCV13, and lineages associated with antimicrobial nonsusceptibility were identified.
Commentary: Complicated Urinary Tract Infections: What's a Lab To Do?
Authors: Brecher Stephen M. 
Published: March 2016

ABSTRACT

The article by Price et al. in this issue (T. K. Price et al., J Clin Microbiol 54:1216–1222, 2016,
http://dx.doi.org/10.1128/JCM.00044-16
) advocates for the use of a larger inoculum when culturing urine obtained by “in-and-out” catheterization in a selected female population. Their findings and the resulting challenges will afford clinical microbiologists and specialty physicians an opportunity to review what will or should be done with the additional microbiological culture data.
Multicenter Evaluation of Clinical Diagnostic Methods for Detection and Isolation of Campylobacter spp. from Stool
Authors: Fitzgerald Collette , Patrick Mary , Gonzalez Anthony , Akin Joshua , Polage Christopher R. , Wymore Kate , Gillim-Ross Laura , Xavier Karen , Sadlowski Jennifer , Monahan Jan , Hurd Sharon , Dahlberg Suzanne , Jerris Robert , Watson Renee , Santovenia Monica , Mitchell David , Harrison Cassandra , Tobin-D'Angelo Melissa , DeMartino Mary , Pentella Michael , Razeq Jafar , Leonard Celere , Jung Carrianne , Achong-Bowe Ria , Evans Yaaqobah , Jain Damini , Juni Billie , Leano Fe , Robinson Trisha , Smith Kirk , Gittelman Rachel M. , Garrigan Charles , Nachamkin Irving 
Published: March 2016

ABSTRACT

The use of culture-independent diagnostic tests (CIDTs), such as stool antigen tests, as standalone tests for the detection of
Campylobacter
in stool is increasing. We conducted a prospective, multicenter study to evaluate the performance of stool antigen CIDTs compared to culture and PCR for
Campylobacter
detection. Between July and October 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of
Campylobacter
selective media, four commercial stool antigen assays, and a commercial PCR assay. Illnesses from which specimens were positive by one or more culture media or at least one CIDT and PCR were designated “cases.” A total of 95 specimens (3.4%) met the case definition. The stool antigen CIDTs ranged from 79.6% to 87.6% in sensitivity, 95.9 to 99.5% in specificity, and 41.3 to 84.3% in positive predictive value. Culture alone detected 80/89 (89.9% sensitivity)
Campylobacter
jejuni/Campylobacter coli
-positive cases. Of the 209 noncases that were positive by at least one CIDT, only one (0.48%) was positive by all four stool antigen tests, and 73% were positive by just one stool antigen test. The questionable relevance of unconfirmed positive stool antigen CIDT results was supported by the finding that noncases were less likely than cases to have gastrointestinal symptoms. Thus, while the tests were convenient to use, the sensitivity, specificity, and positive predictive value of
Campylobacter
stool antigen tests were highly variable. Given the relatively low incidence of
Campylobacter
disease and the generally poor diagnostic test characteristics, this study calls into question the use of commercially available stool antigen CIDTs as standalone tests for direct detection of
Campylobacter
in stool.
Functional Transplant of a Dengue Virus Serotype 3 (DENV3)-Specific Human Monoclonal Antibody Epitope into DENV1
Authors: Messer William B. , Yount Boyd L. , Royal Scott R. , de Alwis Ruklanthi , Widman Douglas G. , Smith Scott A. , Crowe James E. , Pfaff Jennifer M. , Kahle Kristen M. , Doranz Benjamin J. , Ibarra Kristie D. , Harris Eva , de Silva Aravinda M. , Baric Ralph S. 
Published: March 2016

ABSTRACT
The four dengue virus (DENV) serotypes, DENV1 through 4, are endemic throughout tropical and subtropical regions of the world. While first infection confers long-term protective immunity against viruses of the infecting serotype, a second infection with virus of a different serotype carries a greater risk of severe dengue disease, including dengue hemorrhagic fever and dengue shock syndrome. Recent studies demonstrate that humans exposed to DENV infections develop neutralizing antibodies that bind to quaternary epitopes formed by the viral envelope (E) protein dimers or higher-order assemblies required for the formation of the icosahedral viral envelope. Here we show that the quaternary epitope target of the human DENV3-specific neutralizing monoclonal antibody (MAb) 5J7 can be partially transplanted into a DENV1 strain by changing the core residues of the epitope contained within a single monomeric E molecule. MAb 5J7 neutralized the recombinant DENV1/3 strain in cell culture and was protective in a mouse model of infection with the DENV1/3 strain. However, the 5J7 epitope was only partially recreated by transplantation of the core residues because MAb 5J7 bound and neutralized wild-type (WT) DENV3 better than the DENV1/3 recombinant. Our studies demonstrate that it is possible to transplant a large number of discontinuous residues between DENV serotypes and partially recreate a complex antibody epitope, while retaining virus viability. Further refinement of this approach may lead to new tools for measuring epitope-specific antibody responses and new vaccine platforms.

IMPORTANCE
Dengue virus is the most important mosquito-borne pathogen of humans worldwide, with approximately one-half the world's population living in regions where dengue is endemic. Dengue immunity following infection is robust and thought to be conferred by antibodies raised against the infecting virus. However, the specific viral components that these antibodies recognize and how they neutralize the virus have been incompletely described. Here we map a region on dengue virus serotype 3 recognized by the human neutralizing antibody 5J7 and then test the functional significance of this region by transplanting it into a serotype 1 virus. Our studies demonstrate a region on dengue virus necessary for 5J7 binding and neutralization. Our work also demonstrates the technical feasibility of engineering dengue viruses to display targets of protective antibodies. This technology can be used to develop new dengue vaccines and diagnostic assays.
Vaccination with Live Attenuated Simian Immunodeficiency Virus (SIV) Protects from Mucosal, but Not Necessarily Intravenous, Challenge with a Minimally Heterologous SIV
Authors: Sutton Matthew S. , Burns Charles M. , Weiler Andrea M. , Balgeman Alexis J. , Braasch Andrew , Lehrer-Brey Gabrielle , Friedrich Thomas C. , O'Connor Shelby L. 
Published: March 2016

ABSTRACT
Few studies have evaluated the impact of the viral challenge route on protection against a heterologous simian immunodeficiency virus (SIV) challenge. We vaccinated seven macaques with a live attenuated SIV that differed from SIVmac239Δnef by 24 amino acids, called m3KOΔnef. All animals were protected from an intrarectal SIVmac239 challenge, whereas only four animals were protected from subsequent intravenous SIVmac239 challenge. These data suggest that immune responses elicited by vaccination with live attenuated SIV in an individual animal can confer protection from intrarectal challenge while remaining insufficient for protection from intravenous challenge.

IMPORTANCE
Our study is important because we show that vaccinated animals can be protected from a mucosal challenge with a heterologous SIV, but the same animals are not necessarily protected from intravenous challenge with the same virus. This is unique because in most studies, either vaccinated animals are challenged multiple times by the same route or only a single challenge is performed. An individually vaccinated animal is rarely challenged multiple times by different routes, so protection from different challenge routes cannot be measured in the same animal. Our data imply that vaccine-elicited responses in an individual animal may be insufficient for protection from intravenous challenge but may be suitable for protection from a mucosal challenge that better approximates human immunodeficiency virus (HIV) exposure.
Zika Virus: New Clinical Syndromes and Its Emergence in the Western Hemisphere
Authors: Lazear Helen M. , Diamond Michael S. 
Published: March 2016

ABSTRACTZika virus (ZIKV) had remained a relatively obscure flavivirus until a recent series of outbreaks accompanied by unexpectedly severe clinical complications brought this virus into the spotlight as causing an infection of global public health concern. In this review, we discuss the history and epidemiology of ZIKV infection, recent outbreaks in Oceania and the emergence of ZIKV in the Western Hemisphere, newly ascribed complications of ZIKV infection, including Guillain-Barré syndrome and microcephaly, potential interactions between ZIKV and dengue virus, and the prospects for the development of antiviral agents and vaccines.
Respiratory Syncytial Virus (RSV) Pulmonary Infection in Humanized Mice Induces Human Anti-RSV Immune Responses and Pathology
Authors: Sharma Anurag , Wu Wenzhu , Sung Biin , Huang Jing , Tsao Tiffany , Li Xiangming , Gomi Rika , Tsuji Moriya , Worgall Stefan 
Published: March 2016

ABSTRACT

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease, which causes high rates of morbidity and mortality in infants and the elderly. Models of human RSV pulmonary disease are needed to better understand RSV pathogenesis and to assess the efficacy of RSV vaccines. We assessed the RSV-specific human innate, humoral, and cellular immune responses in humanized mice (mice with a human immune system [HIS mice]) with functional human CD4
+
T and B cells. These mice were generated by introduction of HLA class II genes, various human cytokines, and human B cell activation factor into immunodeficient NOD scid gamma (NSG) mice by the use of an adeno-associated virus vector, followed by engraftment of human hematopoietic stem cells. During the first 3 days of infection, HIS mice lost more weight and cleared RSV faster than NSG mice. Human chemokine (C-C motif) ligand 3 (CCL3) and human interleukin-1β (IL-1β) expression was detected in the RSV-infected HIS mice. The pathological features induced by RSV infection in HIS mice included peribronchiolar inflammation, neutrophil predominance in the bronchioalveolar lavage fluid, and enhanced airway mucus production. Human anti-RSV IgG and RSV-neutralizing antibodies were detected in serum and human anti-RSV mucosal IgA was detected in bronchioalveolar lavage fluid for up to 6 weeks. RSV infection induced an RSV-specific human gamma interferon response in HIS mouse splenocytes. These results indicate that human immune cells can induce features of RSV lung disease, including mucus hyperplasia, in murine lungs and that HIS mice can be used to elicit human anti-RSV humoral and cellular immunity.

IMPORTANCE
Infections with respiratory syncytial virus (RSV) are common and can cause severe lung disease in infants and the elderly. The lack of a suitable animal model with disease features similar to those in humans has hampered efforts to predict the efficacy of novel anti-RSV therapies and vaccines for use in humans. A murine model consisting of mice with a human immune system (HIS mice) could be useful for assessment of RSV disease and anti-RSV responses specific to humans. This study investigates an HIS mouse model to imitate human RSV disease and immune responses. We found that RSV lung infection in HIS mice results in an RSV-specific pathology that mimics RSV disease in humans and induces human anti-RSV immune responses. This model could be useful for better understanding of human RSV disease and for the development of RSV therapies.
Factors in use of family planning services by Syrian women in a refugee camp in Jordan
Authors: West Lucy , Isotta-Day Harriet , Ba-Break Maryam , Morgan Rosemary 
Published: March 2016

BackgroundThe Syrian conflict presents the fastest growing refugee crisis in the world today, with over four million people now displaced outside the country. Existing literature suggests that family planning services are often still neglected in crisis response efforts.MethodsA small-scale qualitative study conducted in May 2013, interviewing Syrian women residing in a Jordanian refugee camp about use and barriers to accessing family planning services.ResultsThe study shows that significant barriers remain, and suggests that international attempts to address refugees’ family planning needs remain inconsistent.ConclusionsSeveral practical measures are identified to address barriers to access, making the article of both practical and academic relevance.
Plasma Anti-Müllerian Hormone Concentrations and Risk of Breast Cancer among Premenopausal Women in the Nurses' Health Studies
Authors: Eliassen A. Heather , Zeleniuch-Jacquotte Anne , Rosner Bernard , Hankinson Susan E. 
Published: March 2016

Abstract
Background: Anti-Müllerian hormone (AMH) is a member of the TGFβ family of growth and differentiation factors with a key role in regulating folliculogenesis. In experimental studies, using supraphysiologic concentrations, AMH inhibits breast cancer growth. However, high levels of AMH were associated with increased breast cancer risk in two prior prospective epidemiologic studies.
Methods: We conducted a nested case–control study of premenopausal plasma AMH and breast cancer risk within the Nurses' Health Study (NHS) and NHSII. In NHS, 32,826 women donated blood samples in 1989–1990; in NHSII, 29,611 women donated samples in 1996–1999. After blood collection and before February 2004 (NHS) or July 2010 (NHSII), 539 cases were diagnosed among women premenopausal at diagnosis, and were matched 1:1 to controls. ORs and 95% confidence intervals (CI) were calculated using unconditional logistic regression, adjusting for matching and breast cancer risk factors.
Results: Higher plasma levels of AMH were associated with increased breast cancer risk (top vs. bottom quintile multivariate OR, 2.20; 95% CI, 1.34–3.63; P trend = 0.001). The association did not vary by invasive versus in situ disease or by estrogen receptor status. Associations were not significantly different by age at blood or diagnosis. Further adjustment for plasma estradiol or testosterone yielded similar results.
Conclusions: Higher circulating AMH levels are associated with increased breast cancer risk among premenopausal women.
Impact: The significant positive association between premenopausal plasma AMH levels and subsequent breast cancer risk before menopause suggests AMH may be useful as a marker of breast cancer risk in younger women. Cancer Epidemiol Biomarkers Prev; 25(5); 854–60. ©2016 AACR.
The Genomic Landscape of Male Breast Cancers
Authors: Piscuoglio Salvatore , Ng Charlotte K.Y. , Murray Melissa P. , Guerini-Rocco Elena , Martelotto Luciano G. , Geyer Felipe C. , Bidard Francois-Clement , Berman Samuel , Fusco Nicola , Sakr Rita A. , Eberle Carey A. , De Mattos-Arruda Leticia , Macedo Gabriel S. , Akram Muzaffar , Baslan Timour , Hicks James B. , King Tari A. , Brogi Edi , Norton Larry , Weigelt Britta , Hudis Clifford A. , Reis-Filho Jorge S. 
Published: March 2016

Abstract
Purpose: Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers.
Experimental Design: All male breast cancers were estrogen receptor–positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor–normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers.
Results: Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A–like or luminal B–like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair–related genes.
Conclusions: Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045–56. ©2016 AACR.
Statistical State Dynamics of Jet–Wave Coexistence in Barotropic Beta-Plane Turbulence
Authors: Constantinou Navid C. , Farrell Brian F. , Ioannou Petros J. 
Published: March 2016

Abstract
Jets coexist with planetary-scale waves in the turbulence of planetary atmospheres. The coherent component of these structures arises from cooperative interaction between the coherent structures and the incoherent small-scale turbulence in which they are embedded. It follows that theoretical understanding of the dynamics of jets and planetary-scale waves requires adopting the perspective of statistical state dynamics (SSD), which comprises the dynamics of the interaction between coherent and incoherent components in the turbulent state. In this work, the stochastic structural stability theory (S3T) implementation of SSD for barotropic beta-plane turbulence is used to develop a theory for the jet–wave coexistence regime by separating the coherent motions consisting of the zonal jets together with a selection of large-scale waves from the smaller-scale motions that constitute the incoherent component. It is found that mean flow–turbulence interaction gives rise to jets that coexist with large-scale coherent waves in a synergistic manner. Large-scale waves that would exist only as damped modes in the laminar jet are found to be transformed into exponentially growing waves by interaction with the incoherent small-scale turbulence, which results in a change in the mode structure, allowing the mode to tap the energy of the mean jet. This mechanism of destabilization differs fundamentally and serves to augment the more familiar S3T instabilities in which jets and waves arise from homogeneous turbulence with the energy source exclusively from the incoherent eddy field and provides further insight into the cooperative dynamics of the jet–wave coexistence regime in planetary turbulence.
Hemiarthroplasty Versus Total Shoulder Arthroplasty for Shoulder Osteoarthritis
Authors: Garcia Grant H. , Liu Joseph N. , Mahony Gregory T. , Sinatro Alec , Wu Hao-Hua , Craig Edward V. , Warren Russell F. , Dines David M. , Gulotta Lawrence V. 
Published: March 2016

Background: Return to activity is a commonly used indication for shoulder hemiarthroplasty (HA) compared with total shoulder arthroplasty (TSA). Despite clinical studies demonstrating better functional outcomes after TSA, the literature has failed to show a difference in return to sports. Purpose: To compare rates of return to sports in a matched cohort of TSA and HA patients with a preoperative diagnosis of glenohumeral osteoarthritis (OA). Study Design: Cohort study; Level of evidence, 3. Methods: A prospectively collected registry was queried retrospectively for consecutive patients who underwent HA. Inclusion criteria were preoperative diagnosis of OA and more than 2 years of follow-up. After meeting the inclusion criteria, all HA patients were statistically matched to a TSA patient. All patients had end-stage OA with significant glenohumeral joint space narrowing. Results: At final follow-up, 40 HA patients and 40 TSA patients were available. The average (±SD) age at surgery was 65.7 ± 10.5 years and 66.2 ± 9.6 years for the HA and TSA groups, respectively ( P = .06). Average follow-up was 62.0 months and 61.1 months for the HA and TSA groups, respectively ( P = .52). Average American Shoulder and Elbow Surgeons scores improved from 36.3 to 70.2 for HA patients and from 34.0 to 78.5 for TSA patients ( P < .001 for both); final scores were not significantly different between groups ( P = .21). Average visual analog scale pain scores improved from 6.3 to 2.2 for HA patients and from 6.1 to 0.6 for TSA patients ( P < .001 for both). HA patients had significantly worse final visual analog scale scores compared with the TSA group ( P = .002). Significantly more TSA patients were satisfied with their surgery compared with HA patients (100% vs 70%) ( P = .01). Of both groups, 65.5% of HA patients (19 of 29) returned to at least 1 sport postoperatively compared with 97.3% of TSA patients (36 of 37) ( P < .001). Average timing for return to full sports was 5.5 ± 4.2 months and 5.4 ± 3.1 months for the HA and TSA groups, respectively ( P = .92). Significantly more TSA patients returned to higher upper extremity use sports ( P = .01). Conclusion: In patients with OA, rate of return to sports was significantly better after TSA compared with HA. HA patients had significantly more pain, worse surgical satisfaction, and decreased ability to return to high upper extremity use sports. For patients with OA who wish to return to sporting activities, these results help manage expectations.