bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis
Authors: Liu Zhi , Liu Wenshu , Ran Chao , Hu Jun , Zhou Zhigang 
Published: March 2016

AbstractIn this study, we investigated the risk associated with suspension of probiotics administration in tilapia, an animal model that may mimic immune-compromised conditions in humans. Tilapias were fed for 14 days using a probiotics-supplemented diet, followed by a three-day suspension of probiotics treatment and a subsequent challenge by Aeromonas hydrophila. Unexpectedly, the suspension of a probiotic strain Lactobacillus plantarum JCM1149 significantly triggered susceptibility of the host to A. hydrophila. We further observed that suspension of JCM1149 resulted in host gut microbiota dysbiosis and the subsequent disorder in the intestinal metabolites (bile acids, amino acids, and glucose) and damage in the intestinal epithelium, giving rise to a condition similar to antibiotics-induced gut dysbiosis, which collectively impaired tilapia’s gut health and resistance to pathogenic challenges. Additionally, we determined that JCM1149 adhered relatively poorly to tilapia intestinal mucosa and was rapidly released from the gastrointestinal tract (GIT) after suspension, with the rapid loss of probiotic strain probably being the direct cause of gut dysbiosis. Finally, three other probiotic Lactobacillus strains with low intestinal mucosa binding activity showed similar rapid loss phenotype following administration suspension, and induced higher host susceptibility to infection, indicating that the risk is a generic phenomenon in Lactobacillus.
The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated
Authors: Jiménez-Soto Luisa F. , Haas Rainer 
Published: March 2016

AbstractCagA is one of the most studied pathogenicity factors of the bacterial pathogen Helicobacter pylori. It is injected into host cells via the H. pylori cag-Type IV secretion system. Due to its association with gastric cancer, CagA is classified as oncogenic protein. At the same time CagA represents the 4th most abundant protein produced by H. pylori, suggesting that high amounts of toxin are required to cause the physiological changes or damage observed in cells. We were able to quantify the injection of CagA into gastric AGS epithelial cells in vitro by the adaptation of a novel protease-based approach to remove the tightly adherent extracellular bacteria. After one hour of infection only 1.5% of the total CagA available was injected by the adherent bacteria, whereas after 3 hours 7.5% was found within the host cell. Thus, our data show that only a surprisingly small amount of the CagA available in the infection is finally injected under in vitro infection conditions.
A MicroRNA-Mediated Insulin Signaling Pathway Regulates the Toxicity of Multi-Walled Carbon Nanotubes in Nematode Caenorhabditis elegans
Authors: Zhao Yunli , Yang Junnian , Wang Dayong 
Published: March 2016

AbstractThe underlying mechanisms for functions of microRNAs (miRNAs) in regulating toxicity of nanomaterials are largely unclear. Using Illumina HiSeqTM 2000 sequencing technique, we obtained the dysregulated mRNA profiling in multi-walled carbon nanotubes (MWCNTs) exposed nematodes. Some dysregulated genes encode insulin signaling pathway. Genetic experiments confirmed the functions of these dysregulated genes in regulating MWCNTs toxicity. In the insulin signaling pathway, DAF-2/insulin receptor regulated MWCNTs toxicity by suppressing function of DAF-16/FOXO transcription factor. Moreover, we raised a miRNAs-mRNAs network involved in the control of MWCNTs toxicity. In this network, mir-355 might regulate MWCNTs toxicity by inhibiting functions of its targeted gene of daf-2, suggesting that mir-355 may regulate functions of the entire insulin signaling pathway by acting as an upregulator of DAF-2, the initiator of insulin signaling pathway, in MWCNTs exposed nematodes. Our results provides highlight on understanding the crucial role of miRNAs in regulating toxicity of nanomaterials in organisms.
Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA
Authors: Schmidt Thomas P. , Perna Anna M. , Fugmann Tim , Böhm Manja , Jan Hiss  , Haller Sarah , Götz Camilla , Tegtmeyer Nicole , Hoy Benjamin , Rau Tilman T. , Neri Dario , Backert Steffen , Schneider Gisbert , Wessler Silja 
Published: March 2016

AbstractThe cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.
Plastic Deformation Modes of CuZr/Cu Multilayers
Authors: Cui Yan , Abad Oscar Torrents , Wang Fei , Huang Ping , Lu Tian-Jian , Xu Ke-Wei , Wang Jian 
Published: March 2016

AbstractWe synthesized CuZr/Cu multilayers and performed nanoindentation testing to explore the dependence of plastic deformation modes on the thickness of CuZr layers. The Cu layers were 18 nm thick and the CuZr layers varied in thickness from 4 nm to 100 nm. We observed continuous plastic co-deformation in the 4 nm and 10 nm CuZr − 18 nm Cu multilayers and plastic-induced shear instability in thick CuZr layers (>20 nm). The plastic co-deformation is ascribed to the nucleation and interaction of shear transformation zones in CuZr layers at the adjacent interfaces, while the shear instability is associated with the nucleation and propagation of shear bands in CuZr layers. Shear bands are initialized in the CuZr layers due to the accumulated glide dislocations along CuZr-Cu interfaces and propagate into adjacent Cu layers via slips on {111} plane non-parallel to the interface. Due to crystallographic constraint of the Cu layers, shear bands are approximately parallel to {111} plane in the Cu layer.
Using gallium‐nitride cascode switching devices for common mode electromagnetic interference reduction in power converters/inverters
Authors: Lin Jhe‐Yu , Chen Dan , Hung Chung‐Wen , Huang Zan 
Published: March 2016

The gallium‐nitride (GaN) cascode switch has received much attention recently for line‐operated medium–high frequency (200 to 500 kHz) medium‐power (200–1000 W) applications. Owing to its device structure, there are two TO‐220 package options available with regard to the tab internal connection, unlike the conventional vertical power MOSFET. It is pointed out in this study that using proper package combination of GaN cascode devices, the electromagnetic interferences can be reduced in power converters/inverters. A 240 W 200 kHz LLC power converter with a front‐end power‐factor‐correction circuit was built for experimental verification of the theory. Significant reduction was observed. Same theory can be applied to other converter/inverter configurations.
Rapid Worsening of Symptoms and High Cell Proliferative Activity in Intra- and Extramedullary Spinal Hemangioblastoma
Authors: Imagama Shiro , Ito Zenya , Ando Kei , Kobayashi Kazuyoshi , Hida Tetsuro , Ito Kenyu , Ishikawa Yoshimoto , Tsushima Mikito , Matsumoto Akiyuki , Nakashima Hiroaki , Wakao Norimitsu , Sakai Yoshihito , Matsuyama Yukihiro , Ishiguro Naoki 
Published: March 2016

Study Design A retrospective analysis of a prospective database. Objective To compare preoperative symptoms, ambulatory ability, intraoperative spinal cord monitoring, and pathologic cell proliferation activity between intramedullary only and intramedullary plus extramedullary hemangioblastomas, with the goal of determining the optimal timing for surgery. Methods The subjects were 28 patients (intramedullary only in 23 cases [group I] and intramedullary plus extramedullary in 5 cases [group IE]) who underwent surgery for spinal hemangioblastoma. Preoperative symptoms, ambulatory ability on the McCormick scale, intraoperative spinal cord monitoring, and pathologic findings using Ki67 were compared between the groups. Results In group IE, preoperative motor paralysis was significantly higher (100 versus 26%, p < 0.005), the mean period from initial symptoms to motor paralysis was significantly shorter (3.5 versus 11.9 months, p < 0.05), and intraoperative spinal cord monitoring aggravation was higher (65 versus 6%, p < 0.05). All 5 patients without total resection in group I underwent reoperation. Ki67 activity was higher in group IE (15% versus 1%, p < 0.05). Preoperative ambulatory ability was significantly poorer in group IE ( p < 0.05), but all cases in this group improved after surgery, and postoperative ambulatory ability did not differ significantly between the two groups. Conclusions Intramedullary plus extramedullary spinal hemangioblastoma is characterized by rapid preoperative progression of symptoms over a short period, severe spinal cord damage including preoperative motor paralysis, and poor gait ability compared with an intramedullary tumor only. Earlier surgery with intraoperative spinal cord monitoring is recommended for total resection and good surgical outcome especially for an IE tumor compared with an intramedullary tumor.
Size and speed of the working stroke of cardiac myosin in situ
Authors: Caremani Marco , Pinzauti Francesca , Reconditi Massimo , Piazzesi Gabriella , Stienen Ger J. M. , Lombardi Vincenzo , Linari Marco 
Published: March 2016

Significance
To our knowledge, this paper represents a major advancement in the physiology and pathophysiology of the heart as it gives the first quantitative description of the working stroke of the motor protein cardiac myosin II. The experiments demonstrate that our sarcomere-level mechanical methods on trabeculae have the full potential for the in situ investigation of cardiomyopathy-causing mutations in cardiac myosin and tests on specific therapeutic interventions.
Low-Intensity, Stocker-Based Channel Catfish Culture
Authors: Green Bartholomew W , Engle Carole R , Lochmann Rebecca , Phillips Harold 
Published: March 2016

Abstract
Low-intensity production of Channel Catfish Ictalurus punctatus is characterized by low stocking rates, low installed aeration capacity, and no automated dissolved oxygen monitoring. Two studies conducted in nine 0.25-acre ponds quantified production characteristics of stocker Channel Catfish stocked for low-intensity food-fish production in single- or multiple-batch culture. In the multiple-batch study, 0.5-lb stockers (carryover fish) were stocked at 4,500 fish/acre and 0.044-lb fingerlings at 6,000 fish/acre. Stockers were grown to mean individual weights of 1.25, 1.75, or 2.25 lb. In the single-batch study, 0.5-lb stockers were stocked at 3,500, 4,500, and 5,500 fish/acre. All fish were fed a feed containing 32% protein daily to apparent satiation. Ponds were harvested in October and fish were weighed. Growth of carryover fish and understock (fingerlings) in multiple-batch culture was linear and growth-curve slopes did not differ significantly. Carryover fish size-class distributions differed significantly among target weights and progressively shifted towards larger size-classes as target weight increased. Stocking rate affected Channel Catfish growth and yield significantly in single-batch culture. Fish stocked at 3,500 fish/acre grew faster than fish at the higher stocking rates. Mean final weight decreased linearly and gross and net yields increased linearly with increased stocking rate. Size-class distributions differed significantly among stocking rates, and the 3,500-fish/acre size-class distribution was shifted towards larger fish compared with those at the other two stocking rates. By early to mid-July, ponds stocked in the spring with 0.5-lb stockers contained biomasses of market-size fish suitable for partial harvest, and at least 22% of the carryover fish exceeded the lower size limit for the processing plant. If fish larger than 1.5 lb are desired, the data indicated partial harvest should be delayed until August. None of the fish harvested exceeded the processors’ preferred size ranges (1.25–4.00 lb/fish). In summary, larger Channel Catfish can be produced successfully using low-intensity, single- or multiple-batch culture.
LS-GKM: a new gkm-SVM for large-scale datasets
Authors: Lee Dongwon 
Published: March 2016

Abstract
Summary: gkm-SVM is a sequence-based method for predicting and detecting the regulatory vocabulary encoded in functional DNA elements, and is a commonly used tool for studying gene regulatory mechanisms. Here we introduce new software, LS-GKM, which removes several limitations of our previous releases, enabling training on much larger scale (LS) datasets. LS-GKM also provides additional advanced gapped k-mer based kernel functions. With these improvements, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.
Availability and implementation: C/C ++ source codes and related scripts are freely available from http://github.com/Dongwon-Lee/lsgkm/, and supported on Linux and Mac OS X.
Contact: dwlee@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Size matters: fishing less and yielding more in smaller-scale fisheries
Authors: de Melo Alves Damasio Ludmila , Lopes Priscila Fabiana Macedo , Pennino Maria Grazia , Carvalho Adriana Rosa , Sumaila Ussif Rashid 
Published: March 2016

Abstract
Several factors influence catches and the sustainability of fisheries, and such factors might be different depending on the scale on which fisheries work. We investigated the existence of possible subdivisions within small-scale fisheries (SSF) themselves, regarding their economic performance and relative social and environmental impacts to understand which categories of these two types of fleets are best positioned to support sustainability. By doing so, we investigated if it is a good strategy for SSF to aim to grow towards larger scales. We obtained economic and ecological data from landing samplings and information on technological efficiency of this fleet, using a northeastern Brazilian state as a case study. We defined a cut-off point to separate the SSF into two categories of boats, according to their size and gear. We compared their cpue and the factors affecting it within each category; we also compared economic (number of boats, number of landings, jobs, gears, catch, travel time and total time of the fishery, revenues, costs, profits, revenue per unit of effort, and profit per unit of effort) and ecological factors (vulnerability of species caught) between the two categories. We found that small boats spent less time fishing and employed comparatively more people per landed value and catch. The cpue and profits of small boats were also higher. Both large and small boats exploit species with the same overall vulnerability. Therefore, being smaller, even within the SSF category, seems to be a more advantageous social and economic strategy for guaranteeing higher catches and more employment opportunities per catch. These findings need to be taken into account when defining new policies, such as the distribution of subsidies that support or not the sustainable use of fishery resources.
The fisheries history of small pelagics in the Northern Mediterranean
Authors: Van Beveren Elisabeth , Fromentin Jean-Marc , Rouyer Tristan , Bonhommeau Sylvain , Brosset Pablo , Saraux Claire 
Published: March 2016

Abstract
Since 2007, the biomass of sardine and anchovy in the NW Mediterranean has remained persistently low, whereas the biomass of the commercially low-valued sprat has exploded. Also, simultaneous decreases in condition, size, and/or age of these populations were observed. Altogether, this resulted in a drop in landings of small pelagics. To understand the amplitude of these events and to provide a baseline scenario against which current changes can be compared, we compiled exceptionally long landing series (1865–2013) of sardine, anchovy, and mackerel for different subregions of the southern French coast. We characterized the fluctuations of these landings and compared these with environmental drivers (sea surface temperature, Rhône river discharge, North Atlantic Oscillation, Western Mediterranean Oscillation—WeMO, and Atlantic Multidecadal Oscillation—AMO), using different time-series analyses. We also collated historical data to infer qualitative changes in fishing effort over time. A fishing effort related increase in landings was observed around 1962 for all three species, although current sardine landings have dropped below levels observed before this period. Sardine and anchovy landings were, respectively, positively and negatively related to the AMO index and anchovy landings were also positively related to the WeMO. We finished by discussing the potential role of the environmental variables and fishing on long-term fishery landings trends.
Object-finding skill created by repeated reward experience
Authors: Ghazizadeh Ali , Griggs Whitney , Hikosaka Okihide 
Published: March 2016

Abstract:For most animals, survival depends on rapid detection of rewarding objects, but search for an object surrounded by many others is known to be difficult and time consuming. However, there is neuronal evidence for robust and rapid differentiation of objects based on their reward history in primates (Hikosaka et al., 2014). We hypothesized that such robust coding should support efficient search for high-value objects, similar to a pop-out mechanism. To test this hypothesis, we let subjects (n=4, macaque monkeys) view a large number of complex objects with consistently biased rewards with variable training durations (1, 5 or >30days). Following training, subjects searched for a high-value object (Good) among a variable number of low-value objects (Bad). Consistent with our hypothesis, we found that Good objects were accurately and quickly targeted, often by a single and direct saccade with a very short latency (<200ms). The dependence of search times on display size reduced significantly with longer reward training, giving rise to a more efficient search (40ms/item to 16ms/item). This object-finding skill showed a large capacity for value-biased objects and was maintained in the long-term memory with no interference from reward learning with other objects. Such object-finding skill, particularly its large capacity and its long term retention, would be crucial for maximizing rewards and biological fitness throughout life where many objects are experienced continuously and/or intermittently.Significance StatementVisual objects that have become associated with reward in the past, can grab our attention even when we are not looking for them. Here, we show that this powerful attentional mechanism serves an important biological purpose: it allows one to quickly find valuable objects regardless of the number of other visual distractors present. Efficient search has long been thought to be primarily limited to objects with certain visually conspicuities (Wolfe and Horowitz, 2004). Our result shows that long-term and consistently biased reward can achieve search efficiencies that are independent of object visual features. This search efficiency is highly scalable as it develops for a large number of objects with no apparent interference between objects and is maintained in long-term memory.
Combating corruption in six Asian countries: a comparative analysis
Authors: Quah Jon S.T. 
Published: March 2016

Purpose
– The purpose of this paper is to compare the experiences of the six Asian countries covered in this special issue and explain their different levels of effectiveness in combating corruption.

Design/methodology/approach
– This paper analyses the policy contexts in these countries, their perceived extent and causes of corruption, and evaluates the effectiveness of their anti-corruption agencies (ACAs).

Findings
– Brunei Darussalam is less corrupt because it is the smallest, least populated and richest country, without being embroiled in conflict compared to the other five larger countries, which are more populous but poorer and adversely affected by conflict. The Sultan’s political will in combating corruption is reflected in the better staffed and funded Anti-Corruption Bureau, which has prosecuted and convicted more corrupt offenders. By contrast, the lack of political will of the governments in the other five countries is manifested in their ineffective ACAs, which are not independent, lack capacity and resources, and are used against political opponents.

Originality/value
– This paper will be useful for those scholars, policy-makers and anti-corruption practitioners interested in how effective these six Asian countries are in combating corruption and the reasons for their different levels of effectiveness.
Jeffrey Pfeffer: stop selling leadership malarkey
Authors: Leavy Brian 
Published: March 2016

Purpose
– For insights into the debate between consultants who advocate authentic, character-based leadership and those that believe leadership is primarily an exercise of political power, S
&
L interviewed Professor Jeffrey Pfeffer, author of Leadership BS: Fixing Workplaces and Careers One Truth at a Time.

Design/methodology/approach
– Professor Pfeffer believes “By any measure or set of relevant measures, the leadership industry has failed and continues to do so.” The interviewer asks him why he reached this conclusion and what implications this has for practitioners.

Findings
– Simply put, leaders need to be true to what others need from them, not to how they may be feeling.

Practical implications
– Professor Pfeffer offers a reminder of the enduring functionality of political skills and acumen in the workplace, which many adherents of the “inspirational leadership” approach don’t seem to want to embrace.

Originality/value
– Professor Pfeffer offers a no-holds-barred account of the intersection of modern workplace realities and self-interested leadership.