bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal Adjuvant Treatment Approach After Upfront Resection of Pancreatic Cancer
Authors: Moaven Omeed , Clark Clancy J. , Russell Gregory B. , Votanopoulos Konstantinos I. , Howerton Russell , Levine Edward A. , Shen Perry
Published: January 2020

Objective:

To identify the survival benefit of different adjuvant approaches and factors influencing their efficacy after upfront resection of pancreatic ductal adenocarcinoma (PDAC).

Summary Background Data:

The optimal adjuvant approach for PDAC remains controversial.

Methods:

Patients from the National Cancer Database who underwent upfront PDAC resection from 2010 to 2014 were analyzed to determine clinical outcomes of different adjuvant treatment approaches, stratified according to pathologic characteristics. Factors associated with overall survival were identified with multivariable logistic regression and Cox proportional hazards were used to compare overall survival of different treatment approaches in the whole cohort, and propensity score matched groups.

Results:

We included 16,709 patients who underwent upfront resection of PDAC. On multivariable analysis, tumor size, grade, positive margin, nodal involvement, lymphovascular invasion (LVI), stage, lymph node ratio, not receiving chemotherapy, and/or radiation were predictors for worse survival. In the presence of at least 1 high-risk pathologic feature (nodal or margin involvement or LVI) chemotherapy with subsequent radiation provided the most significant survival benefit (median survivals: 24.8 vs 21.0 mo for adjuvant chemotherapy; HR = 0.81; 95% CI: 0.77–0.86; P < 0.001 in propensity score matching). The addition of radiation to adjuvant chemotherapy did not significantly improve overall survival in those with no high-risk pathologic features (median survivals: 54.6 vs 42.7 mo for adjuvant chemotherapy; HR=0.90; 95% CI: 0.75–1.08; P = 0.25 in propensity score matching).

Conclusions:

In the presence of any high-risk pathologic features (nodal or margin involvement or LVI), adjuvant chemotherapy followed by radiation provides a better survival advantage over chemotherapy alone after upfront resection of PDAC.
Hospital Volume of Antireflux Surgery in Relation to Endoscopic and Surgical Re-interventions
Authors: Markar Sheraz , Santoni Giola , Maret-Ouda John , Artama Miia , Färkkilä Martti , Lynge Elsebeth , Pukkala Eero , Ness-Jensen Eivind , von Euler-Chelpin My , Lagergren Jesper
Published: January 2020

Objective:

To test the hypothesis that higher hospital volume decreases endoscopic and surgical re-intervention rates after antireflux surgery.

Background:

Antireflux surgery for gastro-esophageal reflux disease is followed by varying rates of re-interventions. Whether hospital volume influences re-intervention rates is uncertain.

Methods:

This population-based cohort study used nationwide data from Denmark, Finland, and Sweden for patients having undergone primary antireflux surgery. Hospitals were divided into tertiles based upon annual volume, that is, 3 equal-sized groups. The outcomes were 30-day surgical re-intervention, endoscopic re-intervention, and secondary antireflux surgery. Multivariable Cox regression provided hazard ratios (HRs) with 95% confidence intervals (CIs) for risk of the first outcome occurrence. Incidence rate ratios were calculated to count all outcome occurrences. All risk estimates were adjusted for age, sex, comorbidity, type of antireflux surgery, year of surgery, and country.

Results:

Among 33,060 patients and a median follow-up of 12 years after antireflux surgery, the frequencies of 30-day re-intervention, endoscopic re-intervention, and secondary antireflux surgery were 1.2%, 4.6%, and 7.0%, respectively. When comparing the highest with the lowest tertiles, higher hospital volume did not decrease HRs of 30-day re-intervention (adjusted HR = 1.14, 95% CI 0.73–1.77), endoscopic re-intervention (HR = 1.21, 95% CI 0.96–1.51), or secondary antireflux surgery (HR = 1.28, 95% CI 1.05–1.54), but rather increased point estimates. The incidence rate ratios showed similar patterns.

Conclusions:

Higher hospital volume of primary antireflux surgery may not decrease risk of endoscopic or surgical re-intervention, suggesting that centralization will not decrease rates of postoperative complications or recurrence of gastro-esophageal reflux disease.
Development and Validation of a Deep Learning CT Signature to Predict Survival and Chemotherapy Benefit in Gastric Cancer
Authors: Jiang Yuming , Jin Cheng , Yu Heng , Wu Jia , Chen Chuanli , Yuan Qingyu , Huang Weicai , Hu Yanfeng , Xu Yikai , Zhou Zhiwei , Fisher George A. , Li Guoxin , Li Ruijiang
Published: January 2020

Objective:

We aimed to develop a deep learning-based signature to predict prognosis and benefit from adjuvant chemotherapy using preoperative computed tomography (CT) images.

Background:

Current staging methods do not accurately predict the risk of disease relapse for patients with gastric cancer.

Methods:

We proposed a novel deep neural network (S-net) to construct a CT signature for predicting disease-free survival (DFS) and overall survival in a training cohort of 457 patients, and independently tested it in an external validation cohort of 1158 patients. An integrated nomogram was constructed to demonstrate the added value of the imaging signature to established clinicopathologic factors for individualized survival prediction. Prediction performance was assessed with respect to discrimination, calibration, and clinical usefulness.

Results:

The DeLIS was associated with DFS and overall survival in the overall validation cohort and among subgroups defined by clinicopathologic variables, and remained an independent prognostic factor in multivariable analysis (P
< 0.001). Integrating the imaging signature and clinicopathologic factors improved prediction performance, with C-indices: 0.792–0.802 versus 0.719–0.724, and net reclassification improvement 10.1%–28.3%. Adjuvant chemotherapy was associated with improved DFS in stage II patients with high-DeLIS [hazard ratio = 0.362 (95% confidence interval 0.149–0.882)] and stage III patients with high- and intermediate-DeLIS [hazard ratio = 0.611 (0.442–0.843); 0.633 (0.433–0.925)]. On the other hand, adjuvant chemotherapy did not affect survival for patients with low-DeLIS, suggesting a predictive effect (P
interaction = 0.048, 0.016 for DFS in stage II and III disease).

Conclusions:

The proposed imaging signature improved prognostic prediction and could help identify patients most likely to benefit from adjuvant chemotherapy in gastric cancer.
The Impact of Intraperitoneal Levobupivacaine on Pain Relief After Laparoscopic Cholecystectomy: A Meta-analysis of Randomized Controlled Studies
Authors: Wei Xuan , Yao Xiaoxiao
Published: January 2020

Introduction:

The influence of intraperitoneal levobupivacaine on pain relief after laparoscopic cholecystectomy remains controversial. We conducted a systematic review and meta-analysis to explore the impact of intraperitoneal levobupivacaine versus placebo on pain intensity after laparoscopic cholecystectomy.

Materials and Methods:

We searched the PubMed, Embase, Web of Science, EBSCO, and Cochrane Library databases through March 2019 for randomized controlled trials assessing the effect of intraperitoneal levobupivacaine versus placebo on pain intensity after laparoscopic cholecystectomy. This meta-analysis is performed using the random-effect model.

Results:

Six randomized controlled trials are included in the meta-analysis. Overall, compared with the control group after laparoscopic cholecystectomy, intraperitoneal levobupivacaine is associated with substantially reduced pain scores at 2 hours [standard mean difference (SMD)=−0.70; 95% confidence interval (CI)=−1.04 to −0.37; P<0.0001], 4 hours (SMD=−0.61; 95% CI=−0.90 to −0.32; P<0.0001), and 12 hours postoperatively (SMD=−0.31; 95% CI=−0.60 to −0.03; P=0.03), and analgesic requirement (SMD=−0.83; 95% CI=−1.48 to −0.19; P=0.01), but reveals no obvious impact on pain scores at 24 hours postoperatively (SMD=0.09; 95% CI=−0.64 to 0.83; P=0.80) and the incidence of nausea or vomiting (risk ratio=0.69; 95% CI=0.40-1.20; P=0.19). Total adverse events in the levobupivacaine group seem to be lower than that in the control group (risk ratio=0.57; 95% CI=0.38-0.85; P=0.006).

Conclusion:

Intraperitoneal levobupivacaine provides additional benefits for pain relief after laparoscopic cholecystectomy.
A Novel Method of Nasojejunal Feeding and Gastric Decompression Using a Double Lumen Silicone Tube for Upper Gastrointestinal Obstruction
Authors: Tan Jih H. , Sivadurai Gunasunthari , Tan Henry C.L. , Tan Yun R. , Jahit Shukri , Hans Alexander Mahendran
Published: January 2020

Background:

Provision of enteral nutrition with jejunal feeding in upper gastrointestinal obstruction is highly recommended. Access to jejunum can be obtained surgically, percutaneously, or endoscopically. Our institution routinely and preferentially utilizes a silicone nasojejunal tube that is inserted past the obstruction endoscopically. We use a custom dual channel tube that allows feeding at the distal tip and another channel 40 cm from the tip that enables decompression proximally. This is a report of our experience with this custom nasojejunal tube.

Methods:

This is a prospective observational study of 201 patients who underwent endoscopic nasojejunal wire-guided feeding tube insertions for obstruction of either the esophagus or the stomach including both benign and malignant pathologies between January 2015 to June 2018 in Hospital Sungai Buloh and Hospital Sultanah Aminah, Malaysia. The indications for tube insertion, insertion technique, and tube-related problems were described.

Results:

The nasojejunal tube was used to establish enteral feeding in patients with obstructing tumors of the distal esophagus in 65 patients (32.3%) and gastric outlet obstruction in 72 patients (35.8%). There were 54 patients (26.9%) who required reinsertion. The most common reason for reinsertion was unintentional dislodgement, where 32 patients (15.9%) followed by tube blockage 20 patients (10.0%). Using our method of advancement under direct vision, we had only 2 cases of malposition due to severely deformed anatomy. We had no incidence of aspiration in this group of patients and overall, the patients tolerated the tube well.

Conclusions:

The novel nasojejunal feeding tube with gastric decompression function is a safe and effective method of delivery of enteral nutrition in patients with upper gastrointestinal obstruction. These tubes if inserted properly are well tolerated with almost no risk of malposition and are tolerated well even for prolonged periods of time until definitive surgery could be performed.
Electroconvulsive Therapy in Veterans Health Administration Hospitals
Authors: Peltzman Talya , Gottlieb Daniel J. , Shiner Brian , Riblet Natalie , Watts Bradley V.
Published: January 2020

Objectives

The body of large-scale, epidemiological research on electroconvulsive therapy (ECT) in the United States is limited. To address this gap, we assessed demographic, clinical, pharmacological, and mental health treatment history as well as 2-year mortality outcomes associated with ECT use in the largest U.S. health care system.

Methods

Among all patients who sought mental health care at Veterans Health Administration (VHA) hospitals in 2012, we used bivariate analyses to compare patients who did and not receive ECT during 2 years of follow-up. Among the population who received ECT, descriptive statistics were calculated to characterize prior mental health treatment patterns and ECT receipt.

Results

0.11% (N = 1616) of all VHA mental health patients in 2012 (N = 1,457,053) received ECT in 2 years of follow-up. There was significant regional variation in provision of ECT. Those who received ECT were more likely to have diagnoses of major depressive, bipolar, and personality disorders and were significantly more likely to have had a recent mental health inpatient stay (risk ratio, 6.94). Receipt of ECT was not associated with a difference in all-cause mortality (risk ratio, 0.88). Thirty-two percent of those who received ECT had no substantial antidepressant or therapy trial in the year before index mental health encounter.

Conclusions

Use of ECT in the VHA is rare. Patients who receive ECT have a complex and high-risk profile, not necessarily consistent with the most common indications for ECT.
Low levels of serum vitamin D in clozapine-treated schizophrenia patients are associated with high levels of the proinflammatory cytokine IL-6
Authors: Krivoy Amir , Satz Joshua , Hornfeld Shay H. , Bar Lior , Gaughran Fiona , Shoval Gal , Hochman Eldar , Weizman Abraham , Taler Michal
Published: January 2020

Low levels of vitamin D are prevalent among patients with schizophrenia and have been linked to the risk and outcome of the disorder. Vitamin D has a regulatory effect on the inflammatory system, which is dysfunctional in schizophrenia. We investigated the association between serum vitamin D levels, inflammatory status, and severity of schizophrenia symptoms. A total of 39 clozapine-treated schizophrenia patients were recruited to the study. Blood samples for biochemical analysis were collected from all participants. Serum levels of vitamin D and cytokines (IL-4, IL-6, IL-10, and TNF-α) were analyzed and the association between biochemical and clinical measures was assessed. Most of the sample (82%) had insufficient levels of vitamin D. There was a significant inverse correlation between serum vitamin D and IL-6 levels (Pearson’s r = −0.38, P < 0.05). Vitamin D levels correlated with the severity of positive symptoms (r = 0.39, P < 0.05). These results suggest that within clozapine-treated schizophrenia patients, high levels of vitamin D are associated with lower serum levels of the proinflammatory cytokine IL-6. This relationship may indicate an immunomodulatory effect of vitamin D in treatment-resistant patients with schizophrenia maintained on clozapine.
A general model of locomotion of brittle stars with a variable number of arms
Authors: Wakita Daiki , Kagaya Katsushi , Aonuma Hitoshi
Published: January 2020

Typical brittle stars have five radially symmetrical arms that coordinate to move the body in a certain direction. However, some species have a variable number of arms, which is a unique trait since intact animals normally have a fixed number of limbs. How does a single species manage different numbers of appendages for adaptive locomotion? We herein describe locomotion inOphiactis brachyaspiswith four, five, six and seven arms to propose a common rule for the movement of brittle stars with different numbers of arms. For this, we mechanically stimulated one arm of individuals to analyse escape direction and arm movement. By gathering quantitative indices and employing Bayesian statistical modelling, we noted a pattern: regardless of the total number of arms, an anterior position emerges at one of the second neighbouring arms to a mechanically stimulated arm, while arms adjacent to the anterior one synchronously work as left and right rowers. We propose a model in which an afferent signal runs clockwise or anticlockwise along the nerve ring while linearly counting how many arms it passes through. With this model, the question on how ‘left and right’ emerges in a radially symmetrical body via a decentralized system is answered.
From obstacle to lynchpin: the evolution of the role of bacteriophage lysogeny in defining and understanding viruses
Authors: Kostyrka Gladys , Sankaran Neeraja
Published: January 2020

The phenomenon of bacteriophage lysogeny has played a vital role in understanding the nature of viruses more generally. Discovered in 1920, the phenomenon was first wielded by its discoverers as a challenge to the idea that bacteriophages might be autonomous infectious agents of exogenous origin, namely viruses. But by the 1950s, lysogeny had come to be understood as a key mechanism through which some bacteriophages interacted with their bacterial hosts. In this paper we consider the history of the status of bacteriophage lysogeny from obstacle to lynchpin in conceiving of viruses, paying particular attention to the contributions of Eugène and Élisabeth Wollman, Macfarlane Burnet and André Lwoff in effecting this transition. As Lwoff is often acknowledged to be the author of the ‘modern’ virus concept, this paper also retraces the precise experimental, theoretical and technical pathways that led him and his collaborators from their studies of lysogeny to the construction of the said concept. We discuss Lwoff's virus concept and the widening impact of his ideas, with special consideration of how lysogeny helped revolutionise the understanding of virus–host-cell relationships in tumour viruses.
Genetic affinity between Ningxia Hui and eastern Asian populations revealed by a set of InDel loci
Authors: Zhou Boyan , Wen Shaoqing , Sun Huilin , Zhang Hong , Shi Ruiming
Published: January 2020

According to historical records, ethnic Hui in China obtained substantial genetic components from western Eurasian populations during their Islamization. However, some scholars believed that the ancestry of Hui people were native Chinese populations. In this context, the formation of Hui is due to simple cultural diffusion rather than demic diffusion. In this study, we examined the forensic and population genetic application of the 30 InDel loci in Hui population from Ningxia Hui Autonomous Region, Northwest China. Genotype analysis of 129 unrelated individuals revealed that all loci were in the Hardy–Weinberg equilibrium in Ningxia Hui. Forensic indices calculated from genotypes demonstrated that this panel, Qiagen DIPplex
®
Investigator kit, was powerful enough to be used in individual identification but not in paternity cases. Through population genetic analysis, we found that Ningxia Hui received much more genetic contributions from East Asian populations than those from western Eurasian populations. Finally, we statistically identified the admixture signal of eastern and western Eurasians, although the latter is weak, in Ningxia Hui via the three-population test. All this evidence suggested that the formation of Ningxia Hui was mainly attributed to the cultural transformation of local Chinese residents with minor gene flow from western Eurasian populations.
Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of
Gammarus pisinnus
and
Gammarus lacustris
Authors: Sun Shengming , Wu Ying , Ge Xianping , Jakovlić Ivan , Zhu Jian , Mahboob Shahid , Al-Ghanim Khalid Abdullah , Al-Misned Fahad , Fu Hongtuo
Published: January 2020

We hypothesized that the mitogenome of
Gammarus lacustris
(GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of
Gammarus pisinnus
(GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55%
atp8
to 76.1%
cox1
). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and
Gammarus fossarum
exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in
atp8
) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining
Gammarus
species populating the same geographical range as GP.
3′,4′-Dihydro-2′H-spiro[indoline-3,1′-isoquinolin]-2-ones as potential anti-cancer agents: synthesis and preliminary screening
Authors: Lobe Maloba M. M. , Efange Simon M. N.
Published: January 2020

Both tetrahydroisoquinolines (THIQs) and oxindoles (OXs) display a broad range of biological activities including anti-cancer activity, and are therefore recognized as two privileged scaffolds in drug discovery. In the present study, 24 3′,4′-dihydro-2′H-spiro[indoline-3,1′-isoquinolin]-2-ones, designed as molecular hybrids of THIQ and OX, were synthesized and screenedin vitroagainst 59 cell lines in the NCI-60 screen. Twenty compounds displayed weak to moderate inhibition of cell proliferation; among them, three compounds displayed at least 50% inhibition of cell proliferation. The compounds appeared to target primarily renal cell cancer lines; however, leukaemia, melanoma, non-small cell lung cancer, prostate, ovarian and even breast cancer cell lines were also affected. Therefore, this class of spirooxindoles may provide useful leads in the search for new anti-cancer agents.
Reconciling periodic rhythms of large-scale biological networks by optimal control
Authors: Yuan Meichen , Qu Junlin , Hong Weirong , Li Pu
Published: January 2020

Periodic rhythms are ubiquitous phenomena that illuminate the underlying mechanism of cyclic activities in biological systems, which can be represented by cyclic attractors of the related biological network. Disorders of periodic rhythms are detrimental to the natural behaviours of living organisms. Previous studies have shown that the state transition from one to another attractor can be accomplished by regulating external signals. However, most of these studies until now have mainly focused on point attractors while ignoring cyclic ones. The aim of this study is to investigate an approach for reconciling abnormal periodic rhythms, such as diminished circadian amplitude and phase delay, to the regular rhythms of complex biological networks. For this purpose, we formulate and solve a mixed-integer nonlinear dynamic optimization problem simultaneously to identify regulation variables and to determine optimal control strategies for state transition and adjustment of periodic rhythms. Numerical experiments are implemented in three examples including a chaotic system, a mammalian circadian rhythm system and a gastric cancer gene regulatory network. The results show that regulating a small number of biochemical molecules in the network is sufficient to successfully drive the system to the target cyclic attractor by implementing an optimal control strategy.
A geometric diffuse-interface method for droplet spreading
Authors: Holm Darryl D. , Náraigh Lennon Ó , Tronci Cesare
Published: January 2020

This paper exploits the theory of geometric gradient flows to introduce an alternative regularization of the thin-film equation valid in the case of large-scale droplet spreading—the geometric diffuse-interface method. The method possesses some advantages when compared with the existing models of droplet spreading, namely the slip model, the precursor-film method and the diffuse-interface model. These advantages are discussed and a case is made for using the geometric diffuse-interface method for the purpose of numerical simulations. The mathematical solutions of the geometric diffuse interface method are explored via such numerical simulations for the simple and well-studied case of large-scale droplet spreading for a perfectly wetting fluid—we demonstrate that the new method reproduces Tanner’s Law of droplet spreading via a simple and robust computational method, at a low computational cost. We discuss potential avenues for extending the method beyond the simple case of perfectly wetting fluids.
Leader–follower consensus on activity-driven networks
Authors: Hasanyan Jalil , Zino Lorenzo , Burbano Lombana Daniel Alberto , Rizzo Alessandro , Porfiri Maurizio
Published: January 2020

Social groups such as schools of fish or flocks of birds display collective dynamics that can be modulated by group leaders, which facilitate decision-making toward a consensus state beneficial to the entire group. For instance, leaders could alert the group about attacking predators or the presence of food sources. Motivated by biological insight on social groups, we examine a stochastic leader–follower consensus problem where information sharing among agents is affected by perceptual constraints and each individual has a different tendency to form social connections. Leveraging tools from stochastic stability and eigenvalue perturbation theories, we study the consensus protocol in a mean-square sense, offering necessary-and-sufficient conditions for asymptotic stability and closed-form estimates of the convergence rate. Surprisingly, the prediction of our minimalistic model share similarities with observed traits of animal and human groups. Our analysis anticipates the counterintuitive result that heterogeneity can be beneficial to group decision-making by improving the convergence rate of the consensus protocol. This observation finds support in theoretical and empirical studies on social insects such as spider or honeybee colonies, as well as human teams, where inter-individual variability enhances the group performance.
Bivalve mollusc circadian clock genes can run at tidal frequency
Authors: Tran Damien , Perrigault Mickael , Ciret Pierre , Payton Laura
Published: January 2020

Marine coastal habitats are complex cyclic environments as a result of sun and moon interactions. In contrast with the well-known circadian orchestration of the terrestrial animal rhythmicity (approx. 24 h), the mechanism responsible for the circatidal rhythm (approx. 12.4 h) remains largely elusive in marine organisms. We revealed in subtidal field conditions that the oyster
Crassostrea gigas
exhibits tidal rhythmicity of circadian clock genes and clock-associated genes. A free-running (FR) experiment showed an endogenous circatidal rhythm. In parallel, we showed in the field that oysters' valve behaviour exhibited a strong tidal rhythm combined with a daily rhythm. In the FR experiment, all behavioural rhythms were circatidal, and half of them were also circadian. Our results fuel the debate on endogenous circatidal mechanisms. In contrast with the current hypothesis on the existence of an independent tidal clock, we suggest that a single ‘circadian/circatidal’ clock in bivalves is sufficient to entrain behavioural patterns at tidal and daily frequencies.
Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels,Dreissena rostriformis bugensisin flowing water
Authors: Blackman Rosetta C , Ling Kar Keun Sean , Harper Lynsey R , Shum Peter , Hänfling Bernd , Handley Lori Lawson
Published: January 2020

The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS – particularly during the early stages of an invasion.

Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR, and passive detection via metabarcoding with conserved primers) for detection of quagga mussel,Dreissena rostriformis bugensis;a high priority INNS, along a density gradient on the River Wraysbury, UK.

All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples, and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor.

Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community, and consequently impacts of INNS.
Effective psychological treatment for PTSD changes the dynamics of specific large-scale brain networks
Authors: Charquero-Ballester Marina , Kleim Birgit , Vidaurre Diego , Ruff Christian , Stark Eloise , Tuulari Jetro J. , McManners Hugh , Bar-Haim Yair , Bouquillon Linda , Moseley Allison , Williams Steven C. R , Woolrich Mark , Kringelbach Morten L , Ehlers Anke
Published: January 2020

Abstract

Very little is known about the role of effective cognitive therapy in reversing imbalances in brain activity after trauma. We hypothesised that exaggerated threat perception characteristic of post-traumatic stress disorder (PTSD), and subsequent recovery from this disorder, are underpinned by changes in the dynamics of large-scale brain networks. Here, we use a novel data-driven approach with high temporal precision to find recurring brain networks from fMRI data and estimate when these networks become active during exposure to either trauma reminders or neutral pictures. We found that PTSD patients spend less time in two default mode sub-networks in contrast to trauma-exposed healthy controls, and that PTSD symptom severity correlates positively with time spent in the salience network during exposure to trauma reminders. The former are important for different aspects of self-referential processing and the latter for detection of threat. Importantly, the decreased time in the default mode sub-networks is rebalanced after successful cognitive therapy for PTSD. Our results show that remittance of PTSD through trauma-focused cognitive therapy is associated with the successful reinstatement of a healthy balance in self-referential and threat detection brain networks.
Structure-function relation of the developing calyx of Held synapsein vivo
Authors: Sierksma Martijn C. , Slotman Johan A. , Houtsmuller Adriaan B. , Borst J. Gerard G.
Published: January 2020

In adult rodents, a principal neuron in the medial nucleus of the trapezoid (MNTB) is generally contacted by a single, giant axosomatic terminal called the calyx of Held. How this one-on-one relation is established is still unknown, but anatomical evidence suggests that during development principal neurons are innervated by multiple calyces, which may indicate calyceal competition. However,in vivoelectrophysiological recordings from principal neurons indicated that only a single strong synaptic connection forms per cell. To test whether a mismatch exists between synaptic strength and terminal size, we compared the strength of synaptic inputs with the morphology of the synaptic terminals.In vivowhole-cell recordings of the MNTB neurons from newborn Wistar rats of either sex were made while stimulating their afferent axons, allowing us to identify multiple inputs. The strength of the strongest input increased to calyceal levels in a few days across cells, while the strength of the second strongest input was stable. The recorded cells were subsequently immunolabeled for vesicular glutamate transporters (VGluT) to reveal axosomatic terminals with structured-illumination microscopy. Synaptic strength of the strongest input was correlated with the contact area of the largest VGluT cluster at the soma (r= 0.8), and no indication of a mismatch between structure and strength was observed. Together, our data agree with a developmental scheme in which one input strengthens and becomes the calyx of Held, but not with multi-calyceal competition.

Key points summary

During development the giant, auditory calyx of Held forms a one-to-one connection with a principal neuron of the medial nucleus of the trapezoid body.

While anatomical studies described that most of the target cells are temporarily contacted by multiple calyces, multi-calyceal innervation was only sporadically observed inin vivorecordings, suggesting a structure-function discrepancy.

We correlated synaptic strength of inputs, identified inin vivorecordings, with post hoc labeling of the recorded neuron and synaptic terminals containing vesicular glutamate transporters (VGluT).

During development only one input increased to the level of the calyx of Held synapse, and its strength correlated with the large VGluT cluster contacting the postsynaptic soma.

As neither competing strong inputs nor multiple large VGluT clusters on a single cell were observed, our findings did not indicate a structure-function discrepancy.
Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins
Authors: Lisitsyna Olga M. , Kurnaeva Margarita A. , Arifulin Eugene A. , Shubina Maria Y. , Musinova Yana R. , Mironov Andrey A. , Sheval Eugene V.
Published: January 2020

The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, was one of the most important events in the evolution of the eukaryotic cell. How the proteins were selected for import into the forming nuclei remains an open question. Here, we demonstrate that functional NLSs may be integrated inside nucleotide-binding domains of both eukaryotic and prokaryotic proteins and may co-evolve with these domains. We propose that the pre-existence of NLSs inside prokaryotic proteins dictated, at least partially, the nuclear proteome composition.
p27 regulates the autophagy-lysosomal pathway via the control of Ragulator and mTOR activity in amino acid deprived cells
Authors: Nowosad Ada , Jeannot Pauline , Callot Caroline , Creff Justine , Perchey Renaud T. , Joffre Carine , Codogno Patrice , Manenti Stephane , Besson Arnaud
Published: January 2020

Autophagy is a catabolic process whereby cytoplasmic components are degraded within lysosomes, allowing cells to maintain energy homeostasis during nutrient depletion. Several studies have shown that the CDK inhibitor p27Kip1promotes starvation-induced autophagy. However, the underlying mechanism remains unknown. Here, we report that in amino acid deprived cells, p27 controls autophagy via an mTORC1-dependent mechanism. During prolonged amino acid starvation, a fraction of p27 is recruited to lysosomes where it interacts with LAMTOR1, a component of the Ragulator complex required for mTORC1 lysosomal localization and activation. p27 binding to LAMTOR1 prevents Ragulator assembly and function and subsequent mTORC1 activation, thereby promoting autophagy. Conversely, upon amino acid withdrawal, p27−/−cells exhibit elevated mTORC1 signaling, impaired lysosomal activity and autophagy, and resistance to apoptosis. This is associated with sequestration of TFEB in the cytoplasm, preventing the induction of lysosomal genes required for lysosomal function. Silencing of LAMTOR1 or mTOR inhibition restores autophagy and induces apoptosis in p27−/−cells. Together, these results reveal a direct, coordinated regulation between the cell cycle and cell growth machineries.
Representation ofk-mer sets using spectrum-preserving string sets
Authors: Rahman Amatur , Medvedev Paul
Published: January 2020

Given the popularity and elegance ofk-mer based tools, finding a space-efficient way to represent a set ofk-mers is important for improving the scalability of bioinformatics analyses. One popular approach is to convert the set ofk-mers into the more compact set of unitigs. We generalize this approach and formulate it as the problem of finding a smallest spectrum-preserving string set (SPSS) representation. We show that this problem is equivalent to finding a smallest path cover in a compacted de Bruijn graph. Using this reduction, we prove a lower bound on the size of the optimal SPSS and propose a greedy method called UST that results in a smaller representation than unitigs and is nearly optimal with respect to our lower bound. We demonstrate the usefulness of the SPSS formulation with two applications of UST. The first one is a compression algorithm, UST-Compress, which we show can store a set ofk-mers using an order-of-magnitude less disk space than other lossless compression tools. The second one is an exact statick-mer membership index, UST-FM, which we show improves index size by 10-44% compared to other state-of-the-art low memory indices. Our tool is publicly available at:https://github.com/medvedevgroup/UST/.
An Active Chemo-mechanical Model to Predict Adhesion and Microenvironmental Regulation of 3D Cell Shapes
Authors: Chen Xingyu , Boekhorst Veronika te , McEvoy Eoin , Friedl Peter , Shenoy Vivek B.
Published: January 2020

Cell shapes are known to regulate cytoskeletal organization, stiffness and the ability of cells to migrate and proliferate. Yet a quantitative understanding of the fundamental biochemical and biophysical mechanisms that determine the cell shapes is currently not available. In this study, we developed a chemo-mechanical feedback model to predict how adhesions and the properties of the 3D microenvironment regulate cell shapes. We find that the cells in 3D collagen matrices remain round or adopt an elongated shape depending on the density of active integrins, the level of contractility regulated by mechanosensitive signaling pathways and the density and mechanics of the matrix. While the formation of actin fibers that run along the cell body mediated by integrins and matrix stiffness drive elongation of cells, the cortical and membrane tension resist elongation. Based on the competition between these mechanisms, we derive phase diagrams for cell shape in the space spanned by the density of active adhesions and the level of biochemical signaling that controls contractility. Our predictions are validated by studying the shapes of HT1080 cells cultured in collagen gels of varying densities and using pharmacological treatments to regulate adhesions and contractility. The predictions of the model are found to be in excellent agreement with our experiments and data reported on a number of cell types in the literature.
The effects of Cl−and direct stray current on soil corrosion of three grounding grid materials
Authors: Zhu Zhiping , Shi Chun , Zhang Yu , Liu Zhifeng
Published: January 2020

Purpose

The purpose of this paper is to study the effects of Cl−and direct stray current on the soil corrosion of three grounding grid materials.

Design/methodology/approach

The electrochemical corrosion properties of three grounding grid materials, which include the Q235 steel, Q235 galvanized flat steel and copper, were measured by means of the weak polarization curve method and electrochemical impedance spectroscopy; the corrosion rate of specimens was calculated using the weight loss method; and the specimen surfaces were characterized using the scanning electron microscopy, energy-dispersive spectroscopy and X-ray diffraction analysis.

Findings

Results showed that both factors, Cl−and direct stray current, can accelerate the corrosion rate of grounding grid materials. The magnitude of DC stray current density affected the mass transfer type and response frequency of the anode and cathode reaction of grounding materials, while the Cl−contents of the soil only affect the mass transfer rate of the electrode material from the electrochemical impedance spectroscopy diagrams. The electric field generated by the DC stray current caused Cl−directed migration. The larger the DC stray current density, the greater the diffusion process and the greater the weight loss rate of the grounding grid materials that would have a logarithmic relationship with the Cl−content at the same DC stray current density. The corrosion resistance of the three materials is copper > Q235 galvanized flat steel > Q235 flat steel.

Originality/value

The paper provides information regarding the relationship among Cl−, direct stray current and corrosion of three grounding grid materials by means of electrochemical impedance spectroscopy. Meanwhile the weight loss rate is the logarithmic relationship with the Cl−content, which is useful for understanding the corrosion mechanism of Q235 steel, Q235 galvanized flat steel and copper under the condition of Cl−and direct stray current in soil.
Corrosion performance of steel reinforcement in concrete admixed with magnesium chloride and sulphate
Authors: U. Raghu Babu , B. Kondraivendhan
Published: January 2020

Purpose

Besides with a large amount of Na+and Cl−ions in seawater, the presence of Mg+2and SO4−2ions builds more complex corrosion mechanism. This paper aims to investigate the corrosion of embedded reinforcement in concrete with the environment of both Cl−and SO4−2anions associated Mg+2cation.

Design/methodology/approach

The concrete specimens were prepared by using ordinary Portland cement (OPC), and OPC blended with metakaolin (MK) for water to cementitious material ratio (w/cm) 0.48 and 0.51. The concrete mixes were contaminated with the addition of MgCl2alone and combined MgCl2and MgSO4in mix water. Reinforcement corrosion was evaluated by half-cell potential and corrosion current densities (Icorr) at regular intervals. Moreover, the influence of cementitious material type, salt type and w/cm ratio on electrical resistivity of concrete was also investigated. The statistical models were developed for electrical resistivity as a function of calcium to aluminium content ratio, compressive strength, w/cm ratio and age of concrete.

Findings

Although the corrosion initiation time increases in the concomitant presence of MgSO4and MgCl2as internal source compared to MgCl2, Icorrvalues are higher in both OPC and MK blended concrete. However, electrical resistivity decreased with addition of MgSO4. MK blended concrete performed better with increased resistivity, corrosion initiation time and decreased Icorrvalues.

Originality/value

This study reports statistical distributions for scattered Icorrof rebar in different concrete mixtures. Stepwise regression models were developed for resistivity by considering the interactions among different variables, which would help to estimate the resistivity through basic information.
Knowledge management processes, knowledge worker satisfaction, and organizational performance
Authors: Sahibzada Umar Farooq , Cai Jianfeng , Latif Khawaja Fawad , Sahibzada Hassam Farooq
Published: January 2020

Purpose

Drawing on the knowledge-based view, the purpose of this paper is to investigate the interrelationship between Knowledge Management (KM) processes, Knowledge Worker Satisfaction (KWS) and Organizational Performance (OP). Additionally, the study further seeks to identify the combinations of KM processes and KWS dimensions that can lead to enhanced OP.

Design/methodology/approach

Data were collected from 248 academics and administration employees of Higher Education Institutions (HEIs). The relationships were tested using SmartPLS 3.2.7. The study also employed fuzzy set Qualitative Comparative Analysis (fsQCA) for examining configurational paths.

Findings

The results of the study revealed that KM processes significantly affect KWS and KWS enhances OP in HEIs. Based on fsQCA, the results revealed multiple configurational paths to improved OP.

Originality/value

There is significant lack of research that ascertains the inter-relationship between KM processes, KWS, and OP. This is one of the initial studies that examines the relationship of KM processes, KWS, and OP in HEI’s. From a methodological perspective, the study contributes by combining symmetric and asymmetric statistical tools in KM literature. fsQCA helps to understand the interactions that might not be immediately obvious through traditional symmetric methods.
Modelling environmental and economic sustainability of logistics
Authors: Arya Pragya , Srivastava Manoj Kumar , Jaiswal Mahadeo P.
Published: January 2020

Purpose

Research on sustainability has progressed from a singular focus on one aspect to a simultaneous focus on more than one aspect of the triple bottom line. However, there is a dearth of research that explains why sustainability-related decisions in business often do not bear the expected results. Research that provides managers with a tool to achieve environmental sustainability of logistics without compromising the economic sustainability is scarce. Hence, the purpose of this paper is to bridge the above gaps and to explore the factors that affect investment in technology to balance environmental and economic sustainability of logistics. A model based on system dynamics approach explains the simultaneous interplay of these factors. Simulating the model helps the managers of logistics function decide the size of investment in technology, to achieve environmental efficiency without negatively influencing the economic performance.

Design/methodology/approach

A model based on system dynamics approach explains the simultaneous interplay of these factors. Simulating the model helps the managers of logistics function decide the size of investment in technology, to achieve ecological efficiency without compromising with the economic performance.

Findings

Collaboration with regulatory authorities and with players within the same industry and across industries is a must so that eco-logistics does not become an economic burden for businesses. The decision to invest in technology for eco-logistics is further accentuated if the technology promises some added economic benefits.

Research limitations/implications

From a theoretical perspective, the research has added to the less extensive literature on system dynamics modelling, which is a mixed methodology, combining both qualitative and quantitative techniques. The research is also one of the few attempts that have attempted to simultaneously study more than one aspects of sustainability in business, quantitatively through simulation. Simulation was demonstrated through a single case study, Future works can aim to apply the causal loop diagram to firms in varied sectors.

Practical implications

The managers can use the causal loop diagram to assess the environmental performance of logistics and decide on appropriate level of investment to balance ecological and economic performance of logistics.

Originality/value

The causal loop diagram has been developed through primary data collection via semi-structured interviews. The results were validated by presenting them to respondents to ensure they represent their view points. The results are, therefore, practical and original. This research does not build upon an existing data set or aims to test the applicability of any existing model. The model for this research has been developed from the grass-roots level.