bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Extent of Resection on Incidence of Postoperative Complications in Patients With Glioblastoma
Authors: Laurent Dimitri , Freedman Rachel , Cope Logan , Sacks Patricia , Abbatematteo Joe , Kubilis Paul , Bova Frank , Rahman Maryam 
Published: July 2019

Abstract

BACKGROUND
Extent of resection (EOR) is well established as correlating with overall survival in patients with glioblastoma (GBM). The impact of EOR on reported quality metrics such as patient safety indicators (PSIs) and hospital-acquired conditions (HACs) is unknown.

OBJECTIVE
To perform a retrospective study to evaluate possible associations between EOR and the incidence of PSIs and HACs.

METHODS
We queried all patients diagnosed with GBM who underwent surgical resection at our institution between January 2011 and May 2017. Pre- and postoperative magnetic resonance images were analyzed for EOR. Each chart was reviewed to determine the incidence of PSIs and HACs.

RESULTS
A total of 284 patients met the inclusion criteria. EOR ranged from 39.00 to 100%, with a median of 99.84% and a mean of 95.7%. There were 16 PSI, and 13 HAC, events. There were no significant differences in the rates of PSIs or HACs when compared between patients stratified by gross total resection (EOR ≥ 95%) and subtotal resection (EOR < 95%). The odds of encountering a PSI or HAC were 2.5 times more likely in the subtotal resection group compared to the gross total resection group (P = .58). After adjusting for confounders, the odds of encountering a PSI or HAC in the subtotal resection group were 3.9 times greater than for the gross total resection group (P < .05).

CONCLUSION
Gross total resection of GBM is associated with a decreased incidence of PSIs and HACs, as compared to subtotal resection.
Knowledge and Practices of Physicians and Nurses Related to Urine Cultures in Catheterized Patients: An Assessment of Adherence to IDSA Guidelines
Authors: Advani Sonali D , Gao Catherine A , Datta Rupak , Sann Lawrence , Smith Cindy , Leapman Michael S , Hittelman Adam B , Sabetta James , Dembry Louise-Marie , Martinello Richard A , Juthani-Mehta Manisha 
Published: July 2019

Abstract

Background
A positive urine culture often drives initiation of antimicrobials even in the absence of symptoms. Our objectives were to evaluate the knowledge and practice patterns related to ordering urine cultures in patients with indwelling urinary catheters.

Methods
We performed chart reviews of catheter-associated urinary tract infections (CAUTIs) at our academic health care system between October 1, 2015, and September 30, 2017, to assess practice patterns related to the assessment of potential CAUTIs. Following this, we surveyed physicians and nurses about indications for ordering urine cultures in catheterized patients between January 11, 2018, and April 17, 2018. The accuracy of these indications was assessed based on Infectious Diseases Society of America CAUTI and asymptomatic bacteriuria guidelines.

Results
On chart review, we identified 184 CAUTIs in 2 years. In 159 episodes (86%), urine cultures were ordered inappropriately. In 114 episodes (62%), CAUTI criteria were met by “pan-culturing” rather than symptom-directed testing. Twenty cases (11%) experienced partial or delayed management of other infections, drug adverse events, and Clostridioides difficile infections (CDIs). On our survey, we received 405 responses, for a response rate of 45.3%. Mean scores varied by occupation and level of training. Nurses were more likely than physicians to consider change in appearance (61% vs 23%; P &lt; .05) and odor (74% vs 42%; P &lt; .05) of urine as indications to order urine cultures.

Conclusions
Our data reveal specific knowledge gaps among physicians and nurses related to ordering urine cultures in catheterized patients. The practice of pan-culturing and inappropriate urine culture orders may contribute to overdiagnosis of surveillance CAUTIs, delay in diagnosis of alternative infections, and excess CDIs.
Centralized Communication of Blood Culture Results Leveraging Antimicrobial Stewardship and Rapid Diagnostics
Authors: Shemanski Shelby , Bennett Nicholas , Essmyer Cynthia , Kennedy Kevin , Buchanan Donna M , Warnes Andrew , Boyd Sarah 
Published: July 2019

Abstract

Objective
This study aimed to determine if integrating antimicrobial stewardship program (ASP) personnel with rapid diagnostic testing resulted in improved outcomes for patients with positive blood cultures.

Method
Beginning in 2016, Saint Luke’s Health System (SLHS) implemented a new process where all positive blood cultures were communicated to ASP personnel or SLHS pharmacy staff. Pharmacists then became responsible for interpreting results, assessing patient specific information, and subsequently relaying culture and treatment information to providers. This was a multisite, pre-post, quasi-experimental study (Pre: August to December 2014; Post: August to December 2016). Patients 18 years of age and older with a positive blood culture during admission were included (2014, n = 218; 2016, n = 286). Coprimary outcomes of time to optimal and appropriate therapy were determined from time of culture positivity via gram stain. Secondary outcomes focused on clinical, process, and fiscal endpoints. A pre-post intervention physician survey was conducted to assess the impact on antimicrobial decision making and perceived effect on patient outcomes.

Results
There was no difference in time to appropriate therapy groups (P = .079). Time to optimal therapy was 9.2 hours shorter in 2016 (P = .004). Provider surveys indicated the process improved communication among clinicians and facilitated a shared decision-making process with a perceived improvement in patient care.

Conclusions
An ASP-led blood culture communication process for patients with positive blood cultures was shown to improve time to optimal therapy, support physicians in their decision making on critical lab data, and improve the care for hospitalized patients.
Brucellosis Presenting as Cholecystitis: A Case Report and Literature Review
Authors: Speiser Lisa , Hsieh Lanny , Huang Susan S , Bittencourt Cassiana , Forthal Donald 
Published: July 2019

AbstractBrucellosis is a zoonotic disease endemic to much of the world. It most often presents with nonspecific symptoms and is a well known cause of undulant fever. Focal forms occur less frequently, with osteoarticular complications being the most common. In this study, we describe a rare case of brucellosis presenting as cholecystitis.
The balancing role of evaluation mechanisms in organizational governance—The case of publicly funded research institutions
Authors: Luo Junwen , Ordóñez-Matamoros Gonzalo , Kuhlmann Stefan 
Published: July 2019

AbstractEvaluation taking place within publicly funded research institutions (PRIs) has been practiced as a useful instrument to justify PRIs’ public funding and to provide evidence for their internal decision-making. The role of evaluation in organizational governance is well-acknowledged as being important in PRIs’ management practices. However, it has not attracted much attention from research evaluation scholars. In this article, we propose that evaluation mechanisms perform a balancing role in organizational governance of PRIs with respect to three main aspects: strategy, funding, and operation, where governance tensions often occur between different stakeholders. This research attempts to contribute to a better understanding of why and how evaluation helps to deal with such governance tensions by looking at three case studies, namely the Max Planck Society (MPG), the Helmholtz Association (HGF), both in Germany, and the Chinese Academy of Sciences (CAS). We illustrate the circumstances and conditions in which evaluation mechanisms, where evaluation procedures and culture are institutionalized and stakeholders’ interactions are facilitated, help indeed to mitigate the governance tensions.
Bibliometric analysis of literature in AIDS-related stigma and discrimination
Authors: Sweileh Waleed M 
Published: July 2019

AbstractStigma and discrimination are major barriers in the global fight against human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS). The aim of this study was to create an analytical inventory of worldwide research output in AIDS-related stigma and discrimination. SciVerse Scopus was used for the study period from 1980 to 2017 to retrieve literature in AIDS-related stigma and discrimination. Results were presented as bibliometric tables and maps. In total, 2,509 documents were retrieved. Approximately 40% (n = 990) of the retrieved documents were published in the last 5 years (2013–2017). Retrieved documents received an average of 19.8 citations per article and had an average of 3.2 authors per article. The Hirsh index of the retrieved documents was 94. Most frequently encountered topics were mental health, adherence, adolescents, women, disclosure, and Africa. The USA contributed to 1,226 (48.9%) documents while the African region contributed to 531 (21.2%) documents. Research collaboration among most active countries was relatively low. Authors and institutions from the USA dominated this field. AIDS Care was the most active journal in publishing documents in this field with 307 (13.4%) documents while documents published in Social Medicine journal received the highest citations. Research in AIDS-related stigma and discrimination had witnessed a noticeable increase in the past decade, but the overall number of publications is considered insignificant relative to the size of the problem and the global number of infected people. There was a relative underpresentation of literature from African region despite the fact that more than two-thirds of HIV-infected people in the world are living in Africa.
Identification, characterization, and application of a highly sensitive lactam biosensor fromPseudomonas putida
Authors: Thompson Mitchell G. , Pearson Allison N. , Barajas Jesus F. , Cruz-Morales Pablo , Sedaghatian Nima , Costello Zak , Garber Megan E. , Incha Matthew R. , Valencia Luis E. , Baidoo Edward E. K. , Martin Hector Garcia , Mukhopadhyay Aindrila , Keasling Jay D. 
Published: July 2019

ABSTRACTCaprolactam is an important polymer precursor to nylon traditionally derived from petroleum and produced on a scale of 5 million tons per year. Current biological pathways for the production of caprolactam are inefficient with titers not exceeding 2 mg/L, necessitating novel pathways for its production. As development of novel metabolic routes often require thousands of designs and result in low product titers, a highly sensitive biosensor for the final product has the potential to rapidly speed up development times. Here we report a highly sensitive biosensor for valerolactam and caprolactam fromPseudomonas putidaKT2440 which is >1000x more sensitive to exogenous ligand than previously reported sensors. Manipulating the expression of the sensoroplR(PP_3516) substantially altered the sensing parameters, with various vectors showing Kdvalues ranging from 700 nM (79.1 μg/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detectin vivoproduction of caprolactam above background at ~6 μg/L. The high sensitivity and range of OplR is a powerful tool towards the development of novel routes to the biological synthesis of caprolactam.
Female × male and male × male interactions have limited influence on competitive fertilization inDrosophila melanogaster
Authors: Lüpold Stefan , Reil Jonathan Bradley , Manier Mollie K. , Zeender Valérian , Belote John M. , Pitnick Scott 
Published: July 2019

AbstractHow males and females contribute to joint reproductive success has been a long-standing question in sexual selection. Under postcopulatory sexual selection (PSS), paternity success is predicted to derive from complex interactions among females engaging in cryptic female choice and males engaging in sperm competition. Such interactions have been identified as potential sources of genetic variation in sexually selected traits but are also expected to inhibit trait diversification. To date, studies of interactions between females and competing males have focused almost exclusively on genotypes and not phenotypic variation in sexually selected traits. Here, we characterize within- and between-sex interactions inDrosophila melanogasterusing isogenic lines with heritable variation in both male and female traits known to influence competitive fertilization. We found surprisingly few genotypic interaction effects on various stages of PSS such as female remating interval, copulation duration, sperm transfer, or sperm storage. Only the timing of female sperm ejection depended on female × male genotypic interactions. By contrast, several reproductive events, including sperm transfer, female sperm ejection and sperm storage, were explained by two- and three-way interactions among sex-specific phenotypes. We also documented complex interactions between the lengths of competing males’ sperm and the female seminal receptacle, which are known to have experienced rapid female-male co-diversification. Our results highlight the non-independence of sperm competition and cryptic female choice and demonstrate that complex interactions between the sexes do not limit the ability of multivariate systems to respond to directional sexual selection.Significance statementFor species with internal fertilization and female promiscuity, postcopulatory sexual selection (PSS) is believed to depend, in part, on complex interactions between rival males and between the sexes. Although little investigated, clarifying such interactions is critical as they may limit the efficacy of PSS in the diversification of reproductive traits (e.g., ejaculate biochemistry and sperm, genitalia and female reproductive tract morphology). Here, we resolve how sex-specific traits and their interactions contribute to key reproductive events and outcomes related to competitive fertilization success, including traits known to have experienced rapid diversification. Our results provide novel insights into the operation and complexity of PSS and demonstrate that the processes of sperm competition and cryptic female choice are not independent selective forces.
Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map
Authors: Cowan Cameron S. , Renner Magdalena , Gross-Scherf Brigitte , Goldblum David , Munz Martin , Krol Jacek , Szikra Tamas , Papasaikas Panagiotis , Cuttat Rachel , Waldt Annick , Diggelmann Roland , Patino-Alvarez Claudia P. , Gerber-Hollbach Nadine , Schuierer Sven , Hou Yanyan , Srdanovic Aldin , Balogh Marton , Panero Riccardo , Hasler Pascal W. , Kusnyerik Akos , Szabo Arnold , Stadler Michael B. , Orgül Selim , Hierlemann Andreas , Scholl Hendrik P. N. , Roma Guglielmo , Nigsch Florian , Roska Botond 
Published: July 2019

SummaryHow closely human organoids recapitulate cell-type diversity and cell-type maturation of their target organs is not well understood. We developed human retinal organoids with multiple nuclear and synaptic layers. We sequenced the RNA of 158,844 single cells from these organoids at six developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable ‘developed’ state at a rate similar to human retina development in vivo and the transcriptomes of organoid cell types converged towards the transcriptomes of adult peripheral retinal cell types. The expression of disease-associated genes was significantly cell-type specific in adult retina and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in adult human retinas.
Description ofKlebsiella spallanzaniisp. nov. and ofKlebsiella pasteuriisp. nov
Authors: Merla Cristina , Rodrigues Carla , Passet Virginie , Corbella Marta , Thorpe Harry A. , Kallonen Teemu V.S. , Zong Zhiyong , Marone Piero , Bandi Claudio , Sassera Davide , Corander Jukka , Feil Edward J. , Brisse Sylvain 
Published: July 2019

AbstractKlebsiella oxytocacauses opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. ThisEnterobacteriaceaespecies is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from,Klebsiella michiganensis(Ko1),Klebsiella oxytoca(Ko2),K. huaxiensis(Ko8) andK. grimontii(Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% withK. huaxiensisand 95.5% withK. grimontii, respectively. In addition, three strains ofK. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human faeces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4 and Ko8 from the otherK. oxytocaspecies. Based on these results, we propose the namesKlebsiella spallanzaniifor the Ko3 phylogroup, with SPARK_775_C1T(CIP 111695T, DSM 109531T) as type strain, andKlebsiella pasteuriifor Ko4, with SPARK_836_C1T(CIP 111696T, DSM 109530T) as type strain. Strains ofK. spallanzaniiwere isolated from human urine, cow faeces and farm surfaces, while strains ofK. pasteuriiwere found in faecal carriage from humans, cows and turtles.Accession numbersThe nucleotide sequences generated in this study were deposited in ENA and are available through the INSDC databases under accession numbersMN091365(SB6411T= SPARK775C1T), MN091366 (SB6412T= SPARK836C1T) and MN104661 to MN104677 (16S rRNA), MN076606 to MN076643 (gyrAandrpoB), and MN030558 to MN030567 (blaOXY). Complete genomic sequences were submitted to European Nucleotide Archive under the BioProject number PRJEB15325.AbbreviationsANI, average nucleotide identity; HCCA, a-cyano-4-hydroxycinnamic acid; isDDH,in silicoDNA-DNA hybridization; SCAI, Simmons citrate agar with inositol; MALDI57 ToF MS: Matrix-assisted laser desorption/ionization time of flight mass spectrometry
Comparison of CPU and GPU Bayesian Estimates of Fibre Orientations from Diffusion MRI
Authors: Kim Danny H.C. , Williams Lynne J. , Hernandez-Fernandez Moises , Bjornson Bruce H. 
Published: July 2019

AbstractBackgroundThe correct estimation of fibre orientations is a crucial step for reconstructing human brain tracts. Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques (bedpostx) is able to estimate several fibre orientations and their diffusion parameters per voxel using Markov Chain Monte Carlo (MCMC) in a whole brain diffusion MRI data, and it is capable of running on GPUs, achieving speed-up of over 100 times compared to CPUs. However, few studies have looked at whether the results from the CPU and GPU algorithms differ. In this study, we compared CPU and GPU bedpostx outputs by running multiple trials of both algorithms on the same whole brain diffusion data and compared each distribution of output using Kolmogorov-Smirnov tests.ResultsWe show that distributions of fibre fraction parameters and principal diffusion direction angles from bedpostx and bedpostx_gpu display few statistically significant differences in shape and are localized sparsely throughout the whole brain. Average output differences are small in magnitude compared to underlying uncertainty.ConclusionsDespite small amount of differences in output between CPU and GPU bedpostx algorithms, results are comparable given the difference in operation order and library usage between CPU and GPU bedpostx.
Target Capture Sequencing UnravelsRubusEvolution
Authors: Carter Katherine A. , Liston Aaron , Bassil Nahla V. , Alice Lawrence A. , Bushakra Jill M. , Sutherland Brittany L. , Mockler Todd C. , Bryant Douglas W. , Hummer Kim E. 
Published: July 2019

AbstractBackgroundRubus(Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation ofRubuschallenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between majorRubusclades; and examine the historical biogeography of species diversification.ResultsTarget capture sequencing identified eight major groups withinRubus. SubgenusOrobatusand Subg.Anoplobatuswere monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels,e.g., Subg.Rubus(blackberries) × Subg.Idaeobatus(raspberries) and Subg.Idaeobatus× Subg.Cylactis(Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus.Rubusspecies diversified greatly in Asia during the Miocene.ConclusionsRubustaxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genusRubusmay have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for furtherRubustaxonomic and phylogenetic research.