bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining Prostate Imaging Reporting and Data System, Histogram Analysis, and Prostate-Specific Antigen Density to Determine the Risk of Prostate Cancer in Patients With Prostate-Specific Antigen of 4 to 20 ng/mL
Authors: Liu Xiaohang , Deng Lin , Zhou Liangping , Peng Weijun 
Published: July 2019

Objective
To develop regression models using Prostate Imaging Reporting and Data System (PI-RADS), histogram analysis, and prostate-specific antigen density (PSAD) to predict prostate cancer (PCa) and clinically significant PCa (CSPCa) in patients with prostate-specific antigen of 4 to 20 ng/mL.

Methods
In total, 195 PCa and 386 noncancer patients with prostate-specific antigen of 4 to 20 ng/mL were divided into development and validation cohorts. Magnetic resonance imaging results of them were assessed by PI-RADS scores and histogram analysis–corrected PI-RADS (PI-RADSh) scores. Diagnostic efficiencies for PCa and CSPCa of these scores plus PSAD were evaluated with logistic regression and receiver operating characteristic curve analysis.

Results
Prostate-specific antigen density + PI-RADSh score showed significantly higher area under the receiver operating characteristic curve for PCa (0.956) and CSPCa (0.960), which were higher than PI-RADS (0.909 and 0.926), PI-RADSh (0.921 and 0.940), and PSAD + PI-RADS (0.943 and 0.949) (all P < 0.05).

Conclusions
Incorporation of PSAD and histogram analysis raised the diagnosis efficiencies of PI-RADS for PCa and CSPCa.
Individualized Delay for Abdominal Computed Tomography Angiography Bolus-Tracking Based on Sequential Monitoring: Increased Aortic Contrast Permits Decreased Injection Rate and Lower Iodine Dose
Authors: Gutjahr Ralf , Fletcher Joel G. , Lee Yong S. , Halaweish Ahmed F. , Suresh Vighnesh , Weber Nikkole M. , Vrtiska Terri J. , Williamson Eric E. , Schmidt Bernhard , McCollough Cynthia H. 
Published: July 2019

Objective
The aim of this study was to determine if computed tomography (CT) angiography using an individualized transition delay (CTA-ID) would facilitate reductions in injection rate and iodine dose.

Methods
The CTA-ID was performed in 20 patients with routine injection rate and iodine dose; 20 patients with injection rate lowered by 1 mL/s; and 40 patients with injection rate lowered by 1 mL/s with 29% less iodine. Routine CTAs in the same or size-matched patients served as controls. Diagnostic image quality and intra-arterial CT numbers were assessed.

Results
The median transition delay between aortic threshold and CTA-ID image acquisition was significantly longer than with conventional bolus tracking (mean increase, 13.3 seconds; P < 0.0001), with image quality being the same or better. Intra-arterial CT numbers were 200 Hounsfield units or greater for 80 of 80 CTA-ID, but not for 6 of 49 (12%) internal control or for 11 of 80 (14%) size-matched control patients.

Conclusion
The CTA-ID bolus-tracking software alters transition delays to permit diagnostic CTA examinations despite slower injection rate and less iodine.
Nonhemorrhagic Adrenal Infarction in Pregnancy: Magnetic Resonance Imaging and Computed Tomography Evaluation
Authors: Hynes Daniel , Jabiev Azad , Catanzano Tara 
Published: July 2019

Abstract
We present the case of unilateral nonhemorrhagic adrenal infarct in a 29-week pregnant 21-year-old woman. The patient presented with right upper quadrant pain, nausea, and vomiting. Ultrasonography of the right upper quadrant and appendix was negative for pathology. Magnetic resonance imaging of the abdomen demonstrated a right nonhemorrhagic adrenal infarct, subsequently confirmed with limited computed tomography of the upper abdomen. This case discusses the clinical presentation and pertinent imaging findings of adrenal infarction in pregnancy.
SEXUAL BEHAVIOURS AND EXPERIENCE OF SEXUAL COERCION AMONG IN-SCHOOL FEMALE ADOLESCENT IN SOUTHWESTERN NIGERIA
Authors: Samuel Babatunde Owolodun , Sanusi R.A 
Published: July 2019

ABSTRACTMost people begin their sexual relationship during adolescence and some get involved in risky life threatening behaviors such as unwanted pregnancies, abortions and sexually transmitted infections. This study was therefore designed to understand the patterns of female adolescents sexual behaviours and sexual coercion experience.A descriptive cross-sectional study was carried out among 1227 in-school adolescents in the three senatorial district of Osun State, Southwestern Nigeria. Multi-stage sampling technique was used to select the respondents, and data were collected with pre-tested, semi-structured questionnaires. The data collected were analysed using Statistical Package for Social Sciences (SPSS version 21).Three hundred and thirty seven (27.5%) were sexually exposed with a mean age of sexual initiation of 14.88±2. 46 years. Of the 337 that were sexually exposed 153(56.5%) initiated sex early between the ages of 10-15 years, while (4.7%) had uses drugs or take alcohol before sexual intercourse. Findings revealed that of those that were sexually exposed, 122(11%) were forced to have sex, 101(9.1%) played sex willingly, while 29(2.6%) felt threatened and 3(0.3%) were convinced with money. The proportion of the respondent who reported rape and abduction was (2.6%).Finding from this study is consistent with earlier studies conducted in many other Nigerian cities which showed that in-school adolescents to be sexually active. There is the need to step up campaigns to address this noticed lapse in behavior among the students in order to arrest the usual consequences of such risky sexual behavior.
Loss of function from widely distributed, synonymous mutations at single codons
Authors: Gupta Kritika , Prabha Jyothi , Chandra Soumyanetra , Khare Shruti , Mohan Sonali Vishwa , Kohli Pehu , Asok Aparna , Gowda Harsha , Ramesh Arati , Varadarajan Raghavan 
Published: July 2019

AbstractMutational tolerance inferred from laboratory-based mutational studies is typically much higher than observed natural sequence variation. Using saturation mutagenesis, we show that the ccdA antitoxin component of the ccdAB toxin-antitoxin system is unusually sensitive to mutation with over 60% of mutations leading to loss of function. Multi-base synonymous mutations at a codon display enhanced propensity to show altered phenotypes, relative to single-base ones. Such mutations modulate RNA structure, leading to altered relative translation efficiencies of the two genes in the operon, and a CcdA:CcdB protein ratio below one. These insights were used to predict and experimentally validate synonymous mutations that lead to loss of function in the unrelated relBE operon as well as the lacZ gene. Thus, synonymous mutations can have significant phenotypic effects, in the absence of overexpression or extraneous reporters. More generally, proteins are likely more sensitive to mutation than inferred from previous saturation mutagenesis studies.
Loss of adaptive capacity in asthmatics revealed by biomarker fluctuation dynamics upon experimental rhinovirus challenge
Authors: Sinha Anirban , Lutter René , Xu Binbin , Dekker Tamara , Dierdorp Barbara , Sterk Peter J. , Frey Urs , Delgado-Eckert Edgar 
Published: July 2019

AbstractAsthma is a dynamic disease, in which lung mechanical and inflammatory processes often interact in a complex, unpredictable manner. We hypothesize that this may be explained by respiratory disease-related systems instability and loss of adaptability to changing environmental conditions, resulting in highly fluctuating biomarkers and symptoms. Using time series of inflammatory (eosinophils, neutrophils, FeNO), clinical and lung function biomarkers (PEF, FVC, and FEV1), we estimated this loss of adaptive capacity (AC) during an experimental perturbation with a rhinovirus in 24 healthy and asthmatic volunteers. Loss of AC was estimated by comparing similarities between pre- and post-challenge time series. Unlike healthy participants, the asthmatic’s post-viral-challenge state resembled significantly more other rhinovirus-infected asthmatics than their own pre-viral-challenge state (hypergeometric-test: p=0.029). This reveals loss of AC, and supports the novel concept that not only single physiological mechanisms, but interacting dynamic disease properties are altered in asthma and contribute to a more vulnerable phenotype.
CNN explains tuning properties of anterior, but not middle, face-processing areas in macaque IT
Authors: Raman Rajani , Hosoya Haruo 
Published: July 2019

AbstractRecent computational studies have emphasized layer-wise quantitative similarity between convolutional neural networks (CNNs) and the primate visual ventral stream. However, whether such similarity holds for the face-selective areas, a subsystem of the higher visual cortex, is not clear. Here, we extensively investigate whether CNNs exhibit tuning properties as previously observed in different macaque face areas. While simulating four past experiments on a variety of CNN models, we sought for the model layer that quantitatively matches the multiple tuning properties of each face area. Our results show that higher model layers explain reasonably well the properties of anterior areas, while no layer simultaneously explains the properties of middle areas, consistently across the model variation. Thus, some similarity may exist between CNNs and the primate face-processing system in the near-goal representation, but much less clearly in the intermediate stages, thus giving motivation for a more comprehensive model for understanding the entire system.
Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea oxygen minimum zone sediments
Authors: Mandal Subhrangshu , Bhattacharya Sabyasachi , Roy Chayan , Rameez Moidu Jameela , Sarkar Jagannath , Fernandes Svetlana , Mapder Tarunendu , Peketi Aditya , Mazumdar Aninda , Ghosh Wriddhiman 
Published: July 2019

ABSTRACTTo explore the potential role of tetrathionate in the sulfur cycle of marine sediments, the population ecology of tetrathionate-forming, oxidizing, and respiring microorganisms was revealed at 15-30 cm resolution along two, ∼3-m-long, cores collected from 530- and 580-mbsl water-depths of Arabian Sea, off India’s west coast, within the oxygen minimum zone (OMZ). Metagenome analysis along the two sediment-cores revealed widespread occurrence of the structural genes that govern these metabolisms; high diversity and relative-abundance was also detected for the bacteria known to render these processes. Slurry-incubation of the sediment-samples, pure-culture isolation, and metatranscriptome analysis, corroborated thein situfunctionality of all the three metabolic-types. Geochemical analyses revealed thiosulfate (0-11.1 μM), pyrite (0.05-1.09 wt %), iron (9232-17234 ppm) and manganese (71-172 ppm) along the two sediment-cores. Pyrites (via abiotic reaction with MnO2) and thiosulfate (via oxidation by chemolithotrophic bacteria prevalentin situ) are apparently the main sources of tetrathionate in this ecosystem. Tetrathionate, in turn, can be either converted to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria); 0-2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. Notably tetrathionate was not detectedin situ- high microbiological and geochemical reactivity of this polythionate is apparently instrumental in the cryptic nature of its potential role as a central sulfur cycle intermediate. Biogeochemical roles of this polythionate, albeit revealed here in the context of OMZ sediments, may well extend to the sulfur cycles of other geomicrobiologically-distinct marine sediment horizons.
Deficiency in Bhlhe40 impairs resistance toH. polygyrus bakeriand reveals novel Csf2rb-dependent regulation of anti-helminth immunity
Authors: Jarjour Nicholas N. , Bradstreet Tara R. , Schwarzkopf Elizabeth A. , Cook Melissa E. , Lai Chin-Wen , Huang Stanley Ching-Cheng , Taneja Reshma , Stappenbeck Thaddeus S. , Van Dyken Steven J. , Urban Joseph F. , Edelson Brian T. 
Published: July 2019

ABSTRACTThe cytokines GM-CSF and IL-5 are thought to possess largely divergent functions despite a shared dependence on the common beta (βC) chain to initiate signaling. Although IL-5 is part of the core type 2 cytokine signature and is required for protection against some helminths, it is dispensable for immunity to others, such asHeligmosomoides polygyrus bakeri(H. polygyrus). Whether this is due to compensatory mechanisms is unclear. The transcription factor Bhlhe40 has been shown to control GM-CSF production and is proposed to be a novel regulator of T helper type 2 cells. We have found that Bhlhe40 is required in T cells for a protective memory response to secondaryH. polygyrusinfection.H. polygyrusrechallenge elicited dramatic Bhlhe40-dependent changes in gene and cytokine expression by lamina propria CD4+T cells andin vitro-polarized TH2 cells, including induction of GM-CSF and maximal production of type 2 cytokines including IL-5. βCchain-deficient, but not GM-CSF-deficient, mice rechallenged withH. polygyrushad severely impaired protective immunity. Our results demonstrate that Bhlhe40 is an essential regulator of TH2 cell immunity during helminth infection and reveal unexpected redundancy of βCchain-dependent cytokines.
The environment selects: Modeling energy allocation in microbial communities under dynamic environments
Authors: da Silva Leonor Guedes , Tomás-Martínez Sergio , van Loosdrecht Mark C.M. , Wahl S. Aljoscha 
Published: July 2019

ABSTRACTWhat will be the best metabolic strategy in a competitive environment where oxygen is periodically unavailable? A few decades ago, an accidental, man-made cyclic anaerobic/aerobic environment selected for Polyphosphate Accumulating Organisms (PAOs) and this strategy is now widely used to allow for Enhanced Biological Phosphorus Removal (EBPR) of wastewater. But could it have been predicted? Here, a dynamic resource allocation modeling formalism was used to analyze the impact of selection pressures on metabolic function. With the same meta-network but modified selective pressures, different successful strategies can be predicted: Polyphosphate-AOs, Glycogen-AOs, Polyhydroxyalkanoate-AOs, and regular aerobic heterotrophs. The results demonstrate how storage metabolism allows for different trade-offs between growth yield, robustness, and competitiveness, and highlight how each metabolic function is an important determining factor for a selective advantage in a given environment. This can be seen as an example of when “Unity in biochemistry” by A.Kluyver meets “Everything is everywhere, but the environment selects” by B.Becking and how microbial ecosystems may be described by the energy allocation phenotype instead of a detailed description of each organism.
Oomycete small RNAs invade the plant RNA-induced silencing complex for virulence
Authors: Dunker Florian , Trutzenberg Adriana , Rothenpieler Jan Samuel , Kuhn Sarah , Pröls Reinhard , Schreiber Tom , Tissier Alain , Hückelhoven Ralph , Weiberg Arne 
Published: July 2019

AbstractFungal small RNAs (sRNAs) hijack the plant RNA silencing pathway to manipulate host gene expression, named cross-kingdom RNA interference (ckRNAi). It is currently unknown how conserved and significant ckRNAi is for microbial virulence. Here, we found for the first time that sRNAs of a pathogen representing the oomycete kingdom invade the host plant’s Argonaute (AGO)/RNA-induced silencing complex. To demonstrate the functionality of the plant-invading oomycete Hyaloperonospora arabidopsidis sRNAs (HpasRNAs), we designed a novel CRISPR endoribonuclease Csy4/GUS repressor reporter to visualize in situ pathogen-induced target suppression in Arabidopsis thaliana host plant. By using 5’ RACE-PCR we demonstrated HpasRNAs-directed cleavage of plant mRNAs. The significant role of HpasRNAs together with AtAGO1 in virulence was demonstrated by plant atago1 mutants and by transgenic Arabidopsis expressing a target mimic to block HpasRNAs, that both exhibited enhanced resistance. Individual HpasRNA plant targets contributed to host immunity, as Arabidopsis gene knockout or HpasRNA-resistant gene versions exhibited quantitative enhanced or reduced susceptibility, respectively. Together with previous reports, we found that ckRNAi is conserved among oomycete and fungal pathogens.
Effects of unilateral cortical resection of the visual cortex on bilateral human white matter
Authors: Maallo Anne Margarette S. , Freud Erez , Liu Tina Tong , Patterson Christina , Behrmann Marlene 
Published: July 2019

AbstractChildren with unilateral resections of ventral occipito-temporal cortex (VOTC) typically do not evince visual perceptual impairments, even when relatively large swathes of VOTC are resected. In search of possible explanations for this behavioral competence, we evaluated white matter microstructure and connectivity in eight pediatric epilepsy patients following unilateral cortical resection and 15 age-matched controls. To uncover both local and broader resection-induced effects, we analyzed tractography data using two complementary approaches. First, the microstructural properties were measured in the inferior longitudinal and the inferior fronto-occipital fasciculi, the major VOTC association tracts. Group differences were only evident in the ipsilesional, and not in the contralesional, hemisphere, and single-subject analyses revealed that these differences were limited to the site of the resection. Second, graph theory was used to characterize the connectivity of the contralesional occipito-temporal regions. There were no changes to the network properties in patients with left VOTC resections nor in patients with resections outside the VOTC, but altered network efficiency was observed in two cases with right VOTC resections. These results suggest that, in many, although perhaps not all, cases of unilateral VOTC resections in childhood, the white matter integrity in the preserved contralesional hemisphere along with residual neural activity might be sufficient for normal visual perception.HighlightsThere is well-circumscribed white matter damage in pediatric epilepsy after surgeryWhite matter pathways are normal distal as well as contralesional to the resectionContralesional network properties differ after left or right hemisphere resectionPreserved cortex and white matter may be sufficient for normal perception
Dynamics and Topology of Human Transcribed Cis-regulatory Elements
Authors: Hirabayashi Shigeki , Bhagat Shruti , Matsuki Yu , Takegami Yujiro , Uehata Takuya , Kanemaru Ai , Itoh Masayoshi , Shirakawa Kotaro , Takaori-Kondo Akifumi , Takeuchi Osamu , Carninci Piero , Katayama Shintaro , Hayashizaki Yoshihide , Kere Juha , Kawaji Hideya , Murakawa Yasuhiro 
Published: July 2019

AbstractPromoters and enhancers are key cis-regulatory elements, but how they orchestrate to generate cell-type-specific transcriptomes remains elusive. We developed a simple and robust approach to globally determine 5’-ends of nascent RNAs (NET-CAGE) in diverse cells and tissues, thereby sensitively detecting unstable transcripts including enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site level, uncovering the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without influence of RNA turnover, and identified enhancer-promoter pairs which were simultaneously activated upon cellular stimulation. By integrating NET-CAGE data with chromatin interaction maps, we revealed that cis-regulatory elements are topologically connected according to their cell-type specificity. We discovered new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our collection of NET-CAGE data from human and mouse significantly expanded the FANTOM5 catalogue of transcribed enhancers, with broad applicability to biomedical research. (148 words)
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Authors: Hadadi Noushin , Pandey Vikash , Chiappino-Pepe Anush , Morales Marian , Gallart-Ayala Hector , Mehl Florence , Ivanisevic Julijana , Sentchilo Vladimir , van der Meer Jan R. 
Published: July 2019

ABSTRACTUnderstanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this data remains formidably challenging to interpret and predict. Here we present a new approach that combines genome-scale metabolic modeling with transcriptomics and exometabolomics, both of which are common tools for studying dynamic population behavior. As a realistic demonstration, we developed a genome-scale model of Pseudomonas veronii 1YdBTEX2, a candidate bioaugmentation agent for accelerated metabolism of mono-aromatic compounds in soil microbiomes, while simultaneously collecting experimental data of P. veronii metabolism during growth phase transitions. Predictions of the P. veronii growth rates and specific metabolic processes from the integrated model closely matched experimental observations. We conclude that integrative and network-based analysis can help build predictive models that accurately capture bacterial adaptation responses. Further development and testing of such models may considerably improve the successful establishment of bacterial inoculants in more complex systems.
Meiotic drive reduces egg-to-adult viability in stalk-eyed flies
Authors: Finnegan Sam Ronan , White Nathan Joseph , Koh Dixon , Camus M. Florencia , Fowler Kevin , Pomiankowski Andrew 
Published: July 2019

AbstractSR meiotic drive is a selfish genetic element located on the X chromosome in a number of species that causes dysfunction of Y-bearing sperm. SR is transmitted to up to 100% of offspring, causing extreme sex ratio bias. SR in several species is found in a stable polymorphism at a moderate frequency, suggesting there must be strong frequency-dependent selection resisting its spread. We investigate the effect of SR on female and male egg-to-adult viability in the Malaysian stalk-eyed fly,Teleopsis dalmanni. SR meiotic drive in this species is old, and appears to be broadly stable at a moderate (~20%) frequency. We use large-scale controlled crosses to estimate the strength of selection acting against SR in female and male carriers. We find that SR reduces the egg-to-adult viability of both sexes. In females, homozygous females experience greater reduction in viability (sf= 0.242) and the deleterious effects of SR are additive (ℎ = 0.511). The male deficit in viability (sm= 0.214) is not different from that in homozygous females. The evidence does not support the expectation that deleterious side-effects of SR are recessive or sex-limited. We discuss how these reductions in egg-to-adult survival, as well as other forms of selection acting on SR, act to maintain SR polymorphism in this species.