bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finally, Bulk Typing of Bacterial Species down to Strain Level using ON-rep-seq
Authors: Krych Łukasz , Castro-Mejía Josué L. , Moesby Daniel N. , Mikkelsen Morten B. , Rasmussen Morten A. , Sykulski Maciej , Nielsen Dennis S. 
Published: August 2018

AbstractDespite the massive developments within culture-independent methods for detection and quantification of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (< 24h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation takes less than 5h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting the random error of reads within peaks of LCp generates a set (∼10 contigs per sample; 300bp - 3Kb) of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation. With benchmarked 288 isolates identified on a single flow cell and a theoretical throughput to evaluate over 1000 isolates, our method allows for detailed bacterial identification for less than 2$ per sample at very high speed.
Chemotactic behaviour ofEscherichia coliat high cell density
Authors: Colin Remy , Drescher Knut , Sourjik Victor 
Published: August 2018

AbstractAt high cell density, swimming bacteria exhibit collective motility patterns, self-organized through physical interactions of a however still debated nature. Although high-density behaviours are frequent in natural situations, it remained unknown how collective motion affects chemotaxis, the main physiological function of motility, which enables bacteria to follow environmental gradients in their habitats. Here, we systematically investigate this question in the model organismEscherichia coli, varying cell density, cell length, and suspension confinement. The characteristics of the collective motion indicate that hydrodynamic interactions between swimmers made the primary contribution to its emergence. We observe that the chemotactic drift is moderately enhanced at intermediate cell densities, peaks, and is then strongly suppressed at higher densities. Numerical simulations reveal that this suppression occurs because the collective motion disturbs the choreography necessary for chemotactic sensing. We suggest that this physical hindrance imposes a fundamental constraint on high-density behaviours of motile bacteria, including swarming and the formation of multicellular aggregates and biofilms.
Sensitive period for cognitive repurposing of human visual cortex
Authors: Kanjlia Shipra , Pant Rashi , Bedny Marina 
Published: August 2018

AbstractStudies of sensory loss are a model for understanding the functional flexibility of human cortex. In congenital blindness, subsets of visual cortex are recruited during higher-cognitive tasks, such as language and math tasks. Is such dramatic functional repurposing possible throughout the lifespan or restricted to sensitive periods in development? We compared visual cortex function in individuals who lost their vision as adults (after age 17) to congenitally blind and sighted blindfolded adults. Participants took part in resting-state and task-based fMRI scans during which they solved math equations of varying difficulty and judged the meanings of sentences. Blindness at any age caused “visual” cortices to synchronize with specific fronto-parietal networks at rest. However, in task-based data, visual cortices showed regional specialization for math and language and load-dependent activity only in congenital blindness. Thus, despite the presence of long-range functional connectivity, cognitive repurposing of human cortex is limited by sensitive periods.
Anti-angiogenic effects of VEGF stimulation on endothelium deficient in phosphoinositide recycling
Authors: Stratman Amber N. , Farrelly Olivia M. , Mikelis Constantinos M. , Miller Mayumi F. , Wang Zhiyong , Pham Van N. , Davis Andrew E. , Burns Margaret C. , Pezoa Sofia A. , Castranova Daniel , Yano Joseph J. , Kilts Tina M. , Davis George E. , Gutkind J. Silvio , Weinstein Brant M. 
Published: August 2018

Anti-angiogenic therapies have generated significant interest for their potential to combat tumor growth (1-6). However, the ability of tumors to overproduce pro-angiogenic ligands and overcome targeted inhibitory therapies has hampered this approach (7, 8). A novel way to circumvent this problem might be to target the resynthesis of critical substrates consumed during intracellular transduction of pro-angiogenic signals in endothelial cells, thus harnessing the tumor’s own production of excess stimulatory ligands to deplete adjacent host endothelial cells of the capacity to respond to these signals (9-12). Here we show using zebrafish and human endothelial cellsin vitrothat endothelial cells deficient inCDP-diacylglycerol synthase 2are uniquely sensitive to increased VEGF stimulation due to a reduced capacity to re-synthesize phosphoinositides, including phosphatidylinositol 4,5-bisphosphate (PIP2) a key substrate for VEGF signal transduction, resulting in VEGF-exacerbated defects in angiogenesis and angiogenic signaling (9-22). Using murine tumor allograft models (23) we show that either systemic or endothelial cell specific suppression of phosphoinositide recycling results in reduced tumor growth and reduced tumor angiogenesis. Our results suggest that inhibition of phosphoinositide recycling may provide a useful anti-angiogenic approach, and highlights the general potential of targeting the resynthesis of rate limiting signaling substrates as a valuable therapeutic strategy.SUMMARY STATEMENTTargeting phosphoinositide recycling during tumor angiogenesis provides a potentially uniquely effective anti-cancer therapy.
Epidemiology of Cancers in Zambia: A Significant Variation in Cancer Incidence and Prevalence across the Nation
Authors: Kalubula Maybin , Shen Heqing , Makasa Mpundu , Liu Longjian 
Published: August 2018

ABSTRACTBackgroundCancers are one of the leading causes of death worldwide. More than two thirds of deaths due to cancers occur in low- and middle-income countries whereZambia belongs. This study therefore sought to assess the epidemiology of cancers in Zambia.MethodsWe conducted a retrospective observational study nested on Zambia National Cancer Registry (ZNCR) histopathological and clinical data from 2007 to 2014. Zambia Central Statistics Office (CSO)demographic datawere used to calculate prevalence and incidence rates of cancers. Age-adjusted rates and case fatality rates were estimated using standard methods. We used a Poisson Approximation for calculating 95% confidence intervals (CI).ResultsThe top seven most cancer prevalent districts in Zambia have been Luangwa, Kabwe, Lusaka, Monze, Mongu, Katete and Chipata. Cervical cancer, prostate cancer, breast cancer and Kaposi’s sarcoma were the top four most prevalent cancers as well as major causes of cancer related deaths in Zambia. Standardised Incidence Rates and 95% CI for the top four cancers were: cervix uteri (186.3; CI = 181.77 – 190.83), prostate (60.03; CI = 57.03 – 63.03), breast (38.08; CI = 36.0 – 40.16) and Kaposi’s sarcoma (26.18; CI = 25.14 – 27.22).CFR were: Leukaemia (38.1%); pancreatic cancer (36.3%); lung cancer (33.3%); and brain, nervous system (30.2%). Cancers were associated with HIV withp-value of 0.000 and Pearson correlation coefficient of 0.818.ConclusionsThe widespread distribution of cancers with high prevalence in the southern zone has been perpetrated by lifestyle and sexual culture as well as geography. Intensifying cancer screening and early detection countrywide as well as changing the lifestyle and sexual culture would greatly help in the reduction of cancer cases in Zambia.
Montastraea cavernosacorallite structure demonstrates distinct morphotypes across shallow and mesophotic depth zones in the Gulf of Mexico
Authors: Studivan Michael S. , Milstein Gillian , Voss Joshua D. 
Published: August 2018

AbstractThis study assessed morphological variation of the depth-generalist coralMontastraea cavernosaacross shallow and mesophotic coral ecosystems in the Gulf of Mexico (GOM) using thirteen corallite metrics. While corallite structure differed significantly across sites, we observed that mean corallite diameters were smaller and spacing was greater in mesophotic corals as compared to shallow corals. Additional corallite variation, including greater mean corallite height of mesophotic samples, are hypothesized to be photoadaptive responses to low light environments. Multivariate analyses also revealed two distinct morphotypes identified by significant variation in corallite spacing with >90% accuracy. A ‘shallow’ morphotype was characterized by larger, more closely-spaced corallites, while a ‘depth-generalist’ type exhibited smaller, further-spaced corallites. Variable presence of morphotypes within some sites suggests genotypic influence on corallite morphology as there was a slight, but significant, impact of morphotype on genetic structure within shallow zones in the Flower Garden Banks. Patterns of increased algal symbiont (Symbiodiniaceae) density and chlorophyll concentration were retained in the depth-generalist morphotype even in shallow zones, identifying multiple photoadaptive strategies between morphotypes. The results of this study suggest that morphological variation amongM. cavernosarepresents a combination of genotypic variation and phenotypic plasticity rather than responses to environmental stimuli alone.
Psidium guajava in the Galapagos Islands: population genetics and history of an invasive species
Authors: Urquía Diego , Gutiérrez Bernardo , Pozo Gabriela , Pozo María José , Espín Analía , de Lourdes Torres María 
Published: August 2018

AbstractThe threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, suggestive of gene flow between them. Populations appear to be distinct between the islands of San Cristobal and Isabela, with the population of Santa Cruz being composed as a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, an independent introduction event for Isabela is also possible. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.
Implantable electrical stimulation bioreactor with liquid crystal polymer based electrodes for enhanced bone regeneration at mandibular large defects in rabbit
Authors: Kim Chaebin , Yang Hoon Joo , Cho Tae Hyung , Lee Beom Seok , Gwon Tae Mok , Shin Soowon , Kim In Sook , Kim Sung June , Hwang Soon Jung 
Published: August 2018

AbstractThe osseous regeneration of large bone defects is still a major clinical challenge in maxillofacial and orthopedic surgery. Our previous studies demonstrated that electrical stimulation (ES) with biphasic current pulse showed proliferative effects on bone cells and enhanced secretion of bone-forming growth factors. This study presents an implantable electrical stimulation bioreactor with electrodes based on liquid crystal polymer (LCP), which has excellent bone-binding property. The bioreactor was implanted into a critical sized bone defect and subjected to ES for one week, where bone regeneration was evaluated four weeks after surgery using micro-CT. The effect of ES via bioreactor was compared with a sham control group and positive control group that received recombinant human bone morphogenetic protein (rhBMP)-2 (20 μg). New bone volume per tissue volume (BV/TV) in the ES and rhBMP-2 groups increased to 171% (p< 0.001) and 210% (p < 0.001), respectively, compared to that in the sham control group. In the histological evaluation, there was no inflammation within bone defects and adjacent to LCP in all groups. This study showed that the ES bioreactor with LCP electrodes could enhance bone regeneration at large bone defects, where LCP can act as a mechanically resistant outer box without inflammation.
Task-specific vision models explain task-specific areas of visual cortex
Authors: Dwivedi Kshitij , Roig Gemma 
Published: August 2018

AbstractComputational models such as deep neural networks (DNN) trained for classification are often used to explain responses of the visual cortex. However, not all the areas of the visual cortex are involved in object/scene classification. For instance, scene selective occipital place area (OPA) plays a role in mapping navigational affordances. Therefore, for explaining responses of such task-specific brain area, we investigate if a model that performs a related task can serve as a better computational model than a model that performs an unrelated task. We found that DNN trained on a task (scene-parsing) related to the function (navigational affordances) of a brain region (OPA) explains its responses better than a DNN trained on a task (scene-classification) which is not explicitly related. In a subsequent analysis, we found that the DNNs that showed high correlation with a particular brain region were trained on a task that was consistent with functions of that brain region reported in previous neuroimaging studies. Our results demonstrate that the task is paramount for selecting a computational model of a brain area. Further, explaining the responses of a brain area by a diverse set of tasks has the potential to shed some light on its functions.Author summaryAreas in the human visual cortex are specialized for specific behaviors either due to supervision and interaction with the world or due to evolution. A standard way to gain insight into the function of these brain region is to design experiments related to a particular behavior, and localize the regions showing significant relative activity corresponding to that behavior. In this work, we investigate if we can figure out the function of a brain area in visual cortex using computational vision models. From our results, we find that explaining responses of a brain region using DNNs trained on a diverse set of possible vision tasks can help us gain insights into its function. The consistency of our results using DNNs with the previous neuroimaging studies suggest that the brain region may be specialized for behavior similar to the tasks for which DNNs showed a high correlation with its responses.
MiR-505-3p is a Repressor of the Puberty Onset in Female Mice miR-505-3p and the puberty onset
Authors: Zhou Yuxun , Tong Li , Wang Maochun , Chang Xueying , Wang Sijia , Li Kai , Xiao Junhua 
Published: August 2018

AbstractPuberty onset is a complex trait regulated by multiple genetic and environmental factors. In this study, we narrowed a puberty related QTL down to a 1.7 Mb region on chromosome X in female mice and inferred miR-505-3p as the functional gene.We conducted ectopic expression of miR-505-3p in the hypothalamus of prepubertal female mice through lentivirus-mediated orthotopic injection. The impact of miR-505-3p on female puberty was evaluated by the measurement of pubertal events and histological analysis. The results showed that female mice with overexpression of miR-505-3p in the hypothalamus manifested later puberty onset timing both in vaginal opening and ovary maturation, followed by weaker fertility lying in the longer interval time between mating and delivery, higher abortion rate and smaller litter size. We also constructed miR-505-3p knockout mice by CRISPR/Cas9 technology. MiR-505-3p knockout female mice showed earlier vaginal opening timing, higher serum gonadotrophin and higher expression of puberty-related gene, as well as its target gene Srsf1 in the hypothalamus than their wild type littermates.Srsf1 was proved to be the target gene of miR-505-3p that played the major role in this process. The results of RIP-seq (RNA Immunoprecipitation-sequencing) showed that SF2, the protein product of Srsf1 gene, mainly bound to ribosome protein (RP) mRNAs in GT1-7 cells. The collective evidence implied that miR-505-3p/SRSF1/RP could play a role in the sexual maturation regulation of mammals.Author summaryThe puberty onset in mammals is a vital biological process that signals the acquisition of reproductive capacity. The initiation of puberty is triggered by the activation of hypothalamic pulsatile GnRH surge. The dysregulation of pubertal development shows relevance to later health risks of type 2 diabetes, cardiovascular disease, breast cancer and other health disorders. Recent progress indicates that a lot of genes play a role in the excitatory or inhibitory regulation of GnRH release. However, the detailed pathway of pubertal timing remains unclear. Our previous studies isolated an X-linked QTL that was associated with the timing of puberty in mice. In this study, we proved that miR-505-3p was a female puberty onset regulator based on data from positional cloning, ectopic expression and knockout mouse models. We also assigned Srsf1 as the functional target gene of miR-505-3p underlying this process. The results of RIP-seq showed that SF2, the protein of Srsf1 gene, preferential bound to ribosome protein (RP) mRNAs in GT1-7 cells. We propose that miR-505-3p/SF2/RP could play a role in the sexual maturation regulation of mammals.
CEO succession puzzle in the Polish capital market
Authors: Byrka-Kita Katarzyna , Czerwiński Mateusz , Preś-Perepeczo Agnieszka , Wiśniewski Tomasz 
Published: August 2018

PurposeThe purpose of this paper is to analyse the market reaction to the appointments of chief executive officers (CEOs) in companies listed on the Warsaw Stock Exchange. The authors focussed on the relationship between the characteristics of a newly appointed CEO and the shareholders’ reactions to the appointment of a CEO.Design/methodology/approachTo measure shareholder reaction, the authors apply an event study methodology. The determinants of reaction are identified on the basis of multi-regression analysis.FindingsThe results reveal a negative market reaction to all CEO appointments, both new appointments and reappointments. Investor reaction is driven more by the financial condition of the company, the company’s market performance and the free float, than by the characteristics of a newly appointed CEO. Neither the origins and generation (age) nor the gender of a CEO influence share prices. The relationship between the educational background of a CEO and shareholders’ reactions is mixed. Furthermore, the appointment of an inexperienced CEO seems to be preferred by investors.Research limitations/implicationsThe study is restricted by certain limitations related to the adopted measures, the single-market research, data gaps and the selection of variables for regression analysis. A further cross-country study including Central and Eastern Europe and/or the transition economies of the Baltic Region is recommended. The relationship between the operating performance of a firm and its internal control mechanisms could be explored.Practical implicationsThe findings might influence the decisions made by company owners and supervisory boards when appointing top executives, and might contribute to a better understanding of how CEO appointments can affect shareholder value creation. The results also provide important guidelines for institutions that oversee the financial system.Originality/valueThe findings of this study are expected to the findings are expected to contribute to the literature on the empirical analysis of the shareholder wealth effect, on signalling theory, on the phenomenon of information asymmetry and on corporate governance. The study covers a full economic cycle of the capital market, including the financial crisis and financial bubbles, and it fills a gap in the research regarding emerging markets and transition economies in Europe.
Alternate beeline diagramming method network analysis for interdependent design entities
Authors: Mujumdar Purva , Maheswari J. Uma 
Published: August 2018

Purpose
The design phase is generally characterized with two-way multiple information exchanges/overlaps between the interdependent entities. In this paper, entity is a generic term to represent teams, components, activities or parameters. Existing approaches can either capture a single overlap or lack practical application in representing multiple overlaps. The beeline diagraming method (BDM) network is efficient in representing multiple overlaps for construction projects. However, it considers any entity as indivisible and cannot distinguish partial criticality of entities. In reality, the design phase in any construction project is driven by need basis and often has numerous interruptions. Hence, there is a need to develop an alternate network analysis for BDM for interruptible execution. The paper aims to discuss these issues.

Design/methodology/approach
A pilot study is conducted to formulate the hypothetical examples. Subsequently, these hypothetical BDM examples are analyzed to trace a pattern for criticality. This pattern study along with the existing precedence diagramming method network analysis enabled to derive new equations for forward pass, backward pass and float. Finally, the proposed concepts are applied to two design cases and reviewed with the design experts.

Findings
The proposed network analysis for BDM is efficient for interruptible entity execution.

Practical implications
The proposed BDM network is an information-intensive network that enables the design participants to view the project holistically. Application to two distinct cases emphasizes that the concept is generic and can be applied to any project that is characterized with beelines.

Originality/value
An alternate network analysis for BDM is investigated for interruptible entity execution. This study also clarifies the related concepts – interdependency, iteration, overlaps and multiple information exchanges/linkages.