bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic characterisation of multidrug-resistant <i>Salmonella enterica</i> serotypes isolated from poultry in Cairo, Egypt
Authors: Abdel-Maksoud Mohammed , Abdel-Khalek Rania , El-Gendy Atef , Gamal Rawia F. , Abdelhady Hemmat M. , House Brent L. 
Published: May 2015

Background: Food-borne diseases pose serious health problems, affecting public health and economic development worldwide.Methods: Salmonella was isolated from samples of chicken parts, skin samples of whole chicken carcasses, raw egg yolks, eggshells and chicken faeces. Resulting isolates were characterised by serogrouping, serotyping, antimicrobial susceptibility testing and detection of extended-spectrum β-lactamase (ESBL) production. Antibiotic resistance genes and integrons were identified by polymerase chain reaction (PCR).Results: The detection rates of Salmonella were 60%, 64% and 62% in chicken parts, skin, and faeces, respectively, whereas the egg yolks and eggshells were uniformly negative. Salmonella Kentucky and S. Enteritidis serotypes comprised 43.6% and 2.6% of the isolates, respectively, whilst S. Typhimurium was absent. Variable resistance rates were observed against 16 antibiotics; 97% were resistant to sulfamethoxazole, 96% to nalidixic acid and tetracycline and 76% to ampicillin. Multidrug resistance was detected in 82% (64/78) of the isolates and ESBL production was detected in 8% (6/78). The β-lactamase blaTEM-1 gene was detected in 57.6% and blaSHV-1 in 6.8% of the isolates, whilst the blaOXA gene was absent. The sul1gene was detected in 97.3% and the sul2 gene in 5.3% of the isolates. Sixty-four of the 78 isolates (82%) were positive for the integrase gene (int I) from class 1 integrons, whilst int II was absent.Conclusion: This study reveals the presence of an alarming number of multidrug-resistant Salmonella isolates in the local poultry markets in Cairo. The high levels of drug resistance suggest an emerging problem that could impact negatively on efforts to prevent and treat poultry and poultry-transmitted human diseases in Egypt.
Kernels in the Category of Formal Group Laws
Authors: Demchenko Oleg , Gurevich Alexander 
Published: May 2015

AbstractFontaine described the category of formal groups over the ring of Witt vectors over a finite field of characteristic p with the aid of triples consisting of the module of logarithms, the Dieudonné module, and the morphism from the former to the latter. We propose an explicit construction for the kernels in this category in term of Fontaine's triples. The construction is applied to the formal norm homomorphism in the case of an unramified extension of ℚp and of a totally ramiûed extension of degree less or equal than p. A similar consideration applied to a global extension allows us to establish the existence of a strict isomorphism between the formal norm torus and a formal group law coming from L-series.
Transforming the Primary Care Training Clinic: New York State’s Hospital Medical Home Demonstration Pilot
Authors: Angelotti Marietta , Bliss Kathryn , Schiffman Dana , Weaver Erin , Graham Laura , Lemme Thomas , Pryor Veronica , Gesten Foster C. 
Published: May 2015

Abstract

Background
Training in patient-centered medical home (PCMH) settings may prepare new physicians to measure quality of care, manage the health of populations, work in teams, and include cost information in decision making. Transforming resident clinics to PCMHs requires funding for additional staff, electronic health records, training, and other resources not typically available to residency programs.

Objective
Describe how a 1115 Medicaid waiver was used to transform the majority of primary care training sites in New York State to the PCMH model and improve the quality of care provided.

Methods
The 2013–2014 Hospital Medical Home Program provided awards to 60 hospitals and 118 affiliated residency programs (training more than 5000 residents) to transform outpatient sites into PCMHs and provide high-quality, coordinated care. Site visits, coaching calls, resident surveys, data reporting, and feedback were used to promote and monitor change in resident continuity and quality of care. Descriptive analyses measured improvements in these areas.

Results
A total of 156 participating outpatient sites (100%) received PCMH recognition. All sites enhanced resident education using PCMH principles through patient empanelment, development of quality dashboards, and transforming resident scheduling and training. Clinical quality outcomes showed improvement across the demonstration, including better performance on colorectal and breast cancer screening rates (rate increases of 13%, P ≤ .001, and 11%, P = .011, respectively).

Conclusions
A 1115 Medicaid waiver is a viable mechanism for states to transform residency clinics to reflect new primary care models. The PCMH transformation of 156 sites led to improvements in resident continuity and clinical outcomes.
Primary Bone Tumors: Epidemiologic Comparison of 9200 Patients Treated at Beijing Ji Shui Tan Hospital, Beijing, China, With 10 165 Patients at Mayo Clinic, Rochester, Minnesota
Authors: Niu Xiaohui , Xu Hairong , Inwards Carrie Y. , Li Yuan , Ding Yi , Letson G. Douglas , Bui Marilyn M. 
Published: May 2015

ContextAlthough primary bone tumors are extremely rare, the literature suggests that there are variations in the epidemiologic characteristics in different populations. The most frequently cited epidemiologic characteristics of primary bone tumors are derived from a large US series (Mayo Clinic), with no comparable study thus far performed in China.ObjectiveTo identify any potential epidemiologic differences between Chinese patients and a US series of patients.DesignWe performed a comparison study between 9200 patients treated at Beijing Ji Shui Tan Hospital (JST) and 10 165 patients treated at Mayo Clinic (MC), Rochester Minnesota. Detailed epidemiologic features were analyzed.ResultsWe found that giant cell tumor and osteosarcoma have significantly higher incidences in the JST than the MC patients (P &lt; .001). However, JST patients had a significantly lower incidence of Ewing sarcoma, chordoma, fibrosarcoma, myeloma, and malignant lymphoma (P &lt; .001). For most benign and malignant bone tumors, the Chinese cohort had a more distinct male predominance than the US cohort. Malignant bone tumors had a monomodal age distribution in the JST patient group, with a bimodal age distribution in the MC cohort. Also, there were was a predilection for tumors of the femur and tibia among the JST patients (P &lt; .001).ConclusionsOur data confirm that epidemiologic variations of primary bone tumors exist in different populations. Factors that may contribute to these observed differences are proposed and discussed.
Direct Conversion of Cord Blood CD34+ Cells Into Neural Stem Cells by OCT4
Authors: Liao Wenbin , Huang Nick , Yu Jingxia , Jares Alexander , Yang Jianchang , Zieve Gary , Avila Cecilia , Jiang Xun , Zhang Xiao-Bing , Ma Yupo 
Published: May 2015

Abstract

Cellular reprogramming or conversion is a promising strategy to generate desired stem cell types from somatic cells. Neural stem cells (NSCs) have the potential to regenerate central nervous system tissue and repair damage in response to injury. However, NSCs are difficult to isolate from human tissues and expand in sufficient quantities for therapy. Here, we report a method to generate neural stem cells from cord blood CD34-positive cells by ectopic expression of OCT4 in a feeder-free system. The induced cells (iNSCs) show a characteristic NSC-like morphology and can be expanded in vitro for more than 20 passages. In addition, the iNSCs are positive for neural stem cell-specific markers such as Nestin and Musashi-1 and are similar in gene expression patterns to a human neural stem cell line. The iNSCs express distinct transcriptional factors for forebrain, hindbrain, and spinal cord regions. Upon differentiation, the iNSCs are able to commit into multilineage mature neural cells. Following in vivo introduction into NOD/SCID mice, iNSCs can survive and differentiate in the mouse brain 3 months post-transplantation. Alternatively, we were also able to derive iNSCs with an episomal vector expressing OCT4. Our results suggest a novel, efficient approach to generate neural precursor cells that can be potentially used in drug discovery or regenerative medicine for neurological disease and injury.

Significance
This study describes a novel method to generate expandable induced neural stem cells from human cord blood cells in a feeder-free system by a single factor, OCT4. The data are promising for future applications that require the generation of large amounts of autologous neural stem cells in disease modeling and regenerative medicine.
VU hidrometeorologijos specialybės studentų baigiamųjų darbų analizė klimato kaitos diskurso kontekste
Authors: Valiuškevičius Gintaras 
Published: May 2015

Straipsnyje pateikiami 1994–2013 m. Vilniaus universiteto hidrometeorologijos studijų programos studentų baigiamųjų darbų struktūrą apibūdinančių charakteristikų analizės rezultatai. Kartu siekiama apibūdinti akademinio klimato kaitos diskurso specifiką. Nustatyta, kad nagrinėtų darbų tematika ir struktūra bei klimato kaitos sąvokos statusas juose tiriamuoju laikotarpiu pakito dėl informacinės ir technologinės plėtros. Rodikliai ypač pakito antroje laikotarpio pusėje: maždaug nuo 2003–2005 m. darbuose pradėta dažniau analizuoti meteorologijos-klimatologijos klausimus (anksčiau dominavo hidrologinės temos), naudoti stacionarių nuolatinių matavimų rezultatus, nagrinėti ilgesnes duomenų sekas, cituoti daugiau literatūros šaltinių anglų kalba. Tyrimas rodo, kad baigiamuosius darbus studentai linkę traktuoti kaip aukšto lygio specializuotus mokslinius tekstus ir juose vengia nepagrįstai vartoti savitus terminus. Dėl argumentų stygiaus terminas „klimato kaita“ dažniausiai vartojamas darbų įvade, dar nepradėjus nagrinėti konkrečių rezultatų.
Metals and metalloids in precipitation collected during CHINARE campaign from Shanghai, China, to Zhongshan Station, Antarctica: Spatial variability and source identification
Authors: Shi G. , Teng J. , Ma H. , Li Y. , Sun B. 
Published: May 2015

AbstractMetals and metalloids in continental precipitation have been widely observed, but the data over open oceans are still very limited. Investigation of metals and metalloids in marine precipitation is of great significance to understand global transport of these elements in the atmosphere and their input fluxes to the oceans. So shipboard sampling of precipitation was conducted during a Chinese National Antarctic Research Expedition campaign from Shanghai, China, to Zhongshan Station, East Antarctica, and 22 samples (including 17 rainfall and 5 snowfall events) were collected and analyzed for concentrations of Pb, Ni, Cr, Cu, Co, Hg, As, Cd, Sb, Se, Zn, Mn, and Ti. Results show that concentrations of both metals and metalloids vary considerably along the cruise, with higher concentrations at coastal sites and lower values on the south Indian Ocean. Although only soluble fractions were determined for elements, concentrations in this study are generally comparable to the reported values of marine rain. Enrichment factor analysis shows that most of metals and metalloids are enriched versus crustal sources, even in the samples collected from remote south Indian Ocean. In addition, metals and metalloids in precipitation are also very enriched above sea‐salt abundance, indicating that impacts of sea‐salt aerosols on their concentrations are negligible. Main sources of metals and metalloids were explored with the aid of multivariate statistical analyses. The results show that human emissions have far‐reaching distribution, which may exert an important influence on the solubility of elements in precipitation. This investigation provides valuable information on spatial variation and possible sources of trace elements in precipitation over the open oceans corresponding to understudied region.
RACORO continental boundary layer cloud investigations: 2. Large‐eddy simulations of cumulus clouds and evaluation with in situ and ground‐based observations
Authors: Endo Satoshi , Fridlind Ann M. , Lin Wuyin , Vogelmann Andrew M. , Toto Tami , Ackerman Andrew S. , McFarquhar Greg M. , Jackson Robert C. , Jonsson Haflidi H. , Liu Yangang 
Published: May 2015

AbstractA 60 h case study of continental boundary layer cumulus clouds is examined using two large‐eddy simulation (LES) models. The case is based on observations obtained during the RACORO Campaign (Routine Atmospheric Radiation Measurement (ARM) Aerial Facility (AAF) Clouds with Low Optical Water Depths (CLOWD) Optical Radiative Observations) at the ARM Climate Research Facility's Southern Great Plains site. The LES models are driven by continuous large‐scale and surface forcings and are constrained by multimodal and temporally varying aerosol number size distribution profiles derived from aircraft observations. We compare simulated cloud macrophysical and microphysical properties with ground‐based remote sensing and aircraft observations. The LES simulations capture the observed transitions of the evolving cumulus‐topped boundary layers during the three daytime periods and generally reproduce variations of droplet number concentration with liquid water content (LWC), corresponding to the gradient between the cloud centers and cloud edges at given heights. The observed LWC values fall within the range of simulated values; the observed droplet number concentrations are commonly higher than simulated, but differences remain on par with potential estimation errors in the aircraft measurements. Sensitivity studies examine the influences of bin microphysics versus bulk microphysics, aerosol advection, supersaturation treatment, and aerosol hygroscopicity. Simulated macrophysical cloud properties are found to be insensitive in this nonprecipitating case, but microphysical properties are especially sensitive to bulk microphysics supersaturation treatment and aerosol hygroscopicity.
Hydraulics of floods upstream of horseshoe canyons and waterfalls
Authors: Lapotre Mathieu G. A. , Lamb Michael P. 
Published: May 2015

AbstractHorseshoe waterfalls are ubiquitous in natural streams, bedrock canyons, and engineering structures. Nevertheless, water flow patterns upstream of horseshoe waterfalls are poorly known and likely differ from the better studied case of a one‐dimensional linear step because of flow focusing into the horseshoe. This is a significant knowledge gap because the hydraulics at waterfalls controls sediment transport and bedrock incision, which can compromise the integrity of engineered structures and influence the evolution of river canyons on Earth and Mars. Here we develop new semiempirical theory for the spatial acceleration of water upstream of, and the cumulative discharge into, horseshoe canyons and waterfalls. To this end, we performed 110 numerical experiments by solving the 2‐D depth‐averaged shallow‐water equations for a wide range of flood depths, widths and discharges, and canyon lengths, widths and bed gradients. We show that the upstream, normal flow Froude number is the dominant control on lateral flow focusing and acceleration into the canyon head and that focusing is limited when the flood width is small compared to a cross‐stream backwater length scale. In addition, for sheet floods much wider than the canyon, flow focusing into the canyon head leads to reduced discharge (and drying in cases) across the canyon sidewalls, which is especially pronounced for canyons that are much longer than they are wide. Our results provide new expectations for morphodynamic feedbacks between floods and topography, and thus canyon formation.
Methane oxidation in the eastern tropical North Pacific Ocean water column
Authors: Pack Mary A. , Heintz Monica B. , Reeburgh William S. , Trumbore Susan E. , Valentine David L. , Xu Xiaomei , Druffel Ellen R. M. 
Published: May 2015

AbstractWe report methane (CH4) concentration and methane oxidation (MOx) rate measurements from the eastern tropical north Pacific (ETNP) water column. This region comprises low‐CH4 waters and a depth interval (~200–760 m) of CH4 supersaturation that is located within a regional oxygen minimum zone (OMZ). MOx rate measurements were made in parallel using tracer‐based methods with low‐level 14C‐CH4 (LL 14C) and 3H‐CH4 (3H). The two tracers showed similar trends in MOx rate with water depth, but consistent with previous work, the LL 14C rates (range: 0.034–15 × 10−3 nmol CH4 L−1 d−1) were systematically slower than the parallel 3H rates (range: 0.098–4000 × 10−3 nmol CH4 L−1 d−1). Priming and background effects associated with the 3H‐CH4 tracer and LL 14C filtering effects are implicated as the cause of the systematic difference. The MOx rates reported here include some of the slowest rates measured in the ocean to date, are the first rates for the ETNP region, and show zones of slow CH4 turnover within the OMZ that may permit CH4 derived from coastal sediments to travel great lateral distances. The MOx rate constants correlate with both CH4 and oxygen concentrations, suggesting that their combined availability regulates MOx rates in the region. Depth‐integrated MOx rates provide an upper limit on the magnitude of regional CH4 sources and demonstrate the importance of water column MOx, even at slow rates, as a sink for CH4 that limits the ocean‐atmosphere CH4 flux in the ETNP region.
Stationary‐phase integrals in the cross correlation of ambient noise
Authors: Boschi Lapo , Weemstra Cornelis 
Published: May 2015

AbstractThe cross correlation of ambient signal allows seismologists to collect data even in the absence of seismic events. “Seismic interferometry” shows that the cross correlation of simultaneous recordings of a random wavefield made at two locations is formally related to the impulse response between those locations. This idea has found many applications in seismology, as a growing number of dense seismic networks become available: cross‐correlating long seismic records, the Green's function between instrument pairs is “reconstructed” and used, just like the seismic recording of an explosion, in tomography, monitoring, etc. These applications have been accompanied by theoretical investigations of the relationship between noise cross correlation and the Green's function; numerous formulations of “ambient noise” theory have emerged, each based on different hypotheses and/or analytical approaches. The purpose of this study is to present most of those approaches together, providing a comprehensive overview of the theory. Understanding the specific hypotheses behind each Green's function recipe is critical to its correct application. Hoping to guide nonspecialists who approach ambient noise theory for the first time, we treat the simplest formulation (the stationary‐phase approximation applied to smooth unbounded media) in detail. We then move on to more general treatments, illustrating that the “stationary‐phase” and “reciprocity theorem” approaches lead to the same formulae when applied to the same scenario. We show that a formal cross correlation/Green's function relationship can be found in complex, bounded media and for nonuniform source distributions. We finally provide the bases for understanding how the Green's function is reconstructed in the presence of scattering obstacles.
Soil surface organic layers in Arctic Alaska: Spatial distribution, rates of formation, and microclimatic effects
Authors: Baughman Carson A. , Mann Daniel H. , Verbyla David L. , Kunz Michael L. 
Published: May 2015

AbstractOrganic layers of living and dead vegetation cover the ground surface in many permafrost landscapes and play important roles in ecosystem processes. These soil surface organic layers (SSOLs) store large amounts of carbon and buffer the underlying permafrost and its contained carbon from changes in aboveground climate. Understanding the dynamics of SSOLs is a prerequisite for predicting how permafrost and carbon stocks will respond to warming climate. Here we ask three questions about SSOLs in a representative area of the Arctic Foothills region of northern Alaska: (1) What environmental factors control the thickness of SSOLs and the carbon they store? (2) How long do SSOLs take to develop on newly stabilized point bars? (3) How do SSOLs affect temperature in the underlying ground? Results show that SSOL thickness and distribution correlate with elevation, drainage area, vegetation productivity, and incoming solar radiation. A multiple regression model based on these correlations can simulate spatial distribution of SSOLs and estimate the organic carbon stored there. SSOLs develop within a few decades after a new, sandy, geomorphic surface stabilizes but require 500–700 years to reach steady state thickness. Mature SSOLs lower the growing season temperature and mean annual temperature of the underlying mineral soil by 8 and 3°C, respectively. We suggest that the proximate effects of warming climate on permafrost landscapes now covered by SSOLs will occur indirectly via climate's effects on the frequency, extent, and severity of disturbances like fires and landslides that disrupt the SSOLs and interfere with their protection of the underlying permafrost.
Word and text processing in acquired prosopagnosia
Authors: Hills Charlotte S. , Pancaroglu Raika , Duchaine Brad , Barton Jason J. S. 
Published: May 2015

ObjectiveA novel hypothesis of object recognition asserts that multiple regions are engaged in processing an object type, and that cerebral regions participate in processing multiple types of objects. In particular, for high‐level expert processing, it proposes shared rather than dedicated resources for word and face perception, and predicts that prosopagnosic subjects would have minor deficits in visual word processing, and alexic subjects would have subtle impairments in face perception. In this study, we evaluated whether prosopagnosic subjects had deficits in processing either the word content or the style of visual text.MethodsEleven prosopagnosic subjects, 6 with unilateral right lesions and 5 with bilateral lesions, participated. In the first study, we evaluated their word length effect in reading single words. In the second study, we assessed their time and accuracy for sorting text by word content independent of style, and for sorting text by handwriting or font style independent of word content.ResultsOnly subjects with bilateral lesions showed mildly elevated word length effects. Subjects were not slowed in sorting text by word content, but were nearly uniformly impaired in accuracy for sorting text by style.InterpretationOur results show that prosopagnosic subjects are impaired not only in face recognition but also in perceiving stylistic aspects of text. This supports a modified version of the many‐to‐many hypothesis that incorporates hemispheric specialization for processing different aspects of visual text. Ann Neurol 2015;78:258–271
A Bioorthogonal Chemical Reporter of Viral Infection
Authors: Neef Anne B. , Pernot Lucile , Schreier Verena N. , Scapozza Leonardo , Luedtke Nathan W. 
Published: May 2015

AbstractPathogen‐selective labeling was achieved by using the novel gemcitabine metabolite analogue 2′‐deoxy‐2′,2′‐difluoro‐5‐ethynyluridine (dF‐EdU) and click chemistry. Cells infected with Herpes Simplex Virus‐1 (HSV‐1), but not uninfected cells, exhibit nuclear staining upon the addition of dF‐EdU and a fluorescent azide. The incorporation of the dF‐EdU into DNA depends on its phosphorylation by a herpes virus thymidine kinase (TK). Crystallographic analyses revealed how dF‐EdU is well accommodated in the active site of HSV‐1 TK, but steric clashes prevent dF‐EdU from binding human TK. These results provide the first example of pathogen‐enzyme‐dependent incorporation and labeling of bioorthogonal functional groups in human cells.