bluuebunny/crossref_metadata_2025 huggingface dataset:
Food webs over time: evaluating structural differences and variability of degree distributions in food webs
Authors: López Daniela N. , Camus Patricio A. , Valdivia Nelson , Estay Sergio A.
Published: December 2018

Ecological networks are usually analyzed as time‐aggregated units, where time‐specific interactions are aggregated into one single network. However, the extent to which the structure of these time‐aggregated networks represents natural community dynamics is poorly understood. Here, we compared the topology, represented as the in‐ and out‐degree, of seasonal and time‐aggregated networks. The statistical distributions of both metrics were compared seasonal networks and the resultant time‐aggregated networks. Our results showed that the exponential models best described the general degree distribution. The functional forms of the in‐ and out‐degree distribution differ significantly. We found that the discrete generalized beta and the exponential models best described the in‐degree and out‐degree distributions, respectively, of both seasonal and time‐aggregated networks. Except for the connectance, all topological descriptors of seasonal networks showed values lower than those of time‐aggregated networks. The a and μ parameters of observed seasonal and time‐aggregated networks were significantly lower than those of a simulated niche model. The structure of seasonal and aggregated networks differed significantly in the values of a and μ parameters, converging toward a common structure only after 18 months of seasonal samplings. Our results highlight the risk of underestimating significant ecological variability when time‐aggregated ecological networks are analyzed.
Use of MRI and FDG‐PET/CT to predict fixation of advanced hypopharyngeal squamous cell carcinoma to prevertebral space
Authors: Meerwein Christian M. , Pizzuto Daniele A. , Vital Domenic , Morand Grégoire B. , Stolzmann Paul , Huber Gerhard F. , Huellner Martin W.
Published: December 2018

Background

We evaluated the ability of different (18F)fluoro‐deoxy‐d‐glucose (FDG)‐positron emission tomography (PET)‐based and magnetic resonance (MR)‐based parameters to identify prevertebral space (PVS) infiltration by hypopharyngeal carcinoma.

Methods

Retrospective study on 59 patients with advanced hypopharyngeal squamous cell carcinoma undergoing cross‐sectional imaging and triple endoscopy for staging.

Results

Obliteration of retropharyngeal fat plane on T1‐weighted MR images was found more often (P < .001) in tumors fixated to the PVS. Complete fat plane obliteration best predicted tumor fixation to PVS (accuracy 99%; CI: 97%‐100%; P < .001). With similar accuracy, PET‐based models predicted PVS fixation (combination of standardized uptake value [SUVmax] of the primary tumor and presence of focal FDG‐uptake in prevertebral muscles [accuracy 98%; CI 94%‐100%; P < .001]; metabolic tumor volume [MTV] [accuracy 98%; CI 95%‐100%; P < .001]).

Conclusion

Both the MR‐based parameter of complete fat plane obliteration and PET‐based models (increased SUVmax in combination with presence of focal FDG‐uptake of prevertebral muscles; increased MTV) predict PVS involvement independently with high accuracy.
Normothermic Machine Perfusion (NMP) Inhibits Proinflammatory Responses in the Liver and Promotes Regeneration
Authors: Jassem Wayel , Xystrakis Emmanuel , Ghnewa Yasmeen G. , Yuksel Muhammed , Pop Oltin , Martinez‐Llordella Marc , Jabri Yamen , Huang Xiaohong , Lozano Juan J. , Quaglia Alberto , Sanchez‐Fueyo Alberto , Coussios Constantin C. , Rela Mohamed , Friend Peter , Heaton Nigel , Ma Yun
Published: December 2018

Liver transplantation (LT) is a successful treatment for patients with liver failure. However, organ shortage results in over 11% of patients losing their chance of a transplant attributed to liver decompensation (LD) and death. Ischemia/reperfusion injury (IRI) following conventional cold storage (CS) is a major cause of injury leading to graft loss after LT. Normothermic machine perfusion (NMP), a method of organ preservation, provides oxygen and nutrition during preservation and allows aerobic metabolism. NMP has recently been shown to enable improved organ utilization and posttransplant outcomes following a phase I and a phase III randomized trial. The aim of the present study is to assess the impact of NMP on reducing IRI and to define the underlying mechanisms. We transplanted and compared 12 NMP with 27 CS‐preserved livers by performing gene microarray, immunoprofiling of hepatic lymphocytes, and immunochemistry staining of liver tissues for assessing necrosis, platelet deposition, and neutrophil infiltration, and the status of steatosis after NMP or CS prereperfusion and postreperfusion. Recipients receiving NMP grafts showed significantly lower peak aspartate aminotransferase (AST) levels than those receiving CS grafts. NMP altered gene‐expression profiles of liver tissue from proinflammation to prohealing and regeneration. NMP also reduced the number of interferon gamma (IFN‐γ) and interleukin (IL)‐17–producing T cells and enlarged the CD4posCD25highCD127negFOXP3pos regulatory T cell (Treg) pool. NMP liver tissues showed less necrosis and apoptosis in the parenchyma and fewer neutrophil infiltration compared to CS liver tissues. Conclusion: Reduced IRI in NMP recipients was the consequence of the combination of inhibiting inflammation and promoting graft regeneration.
Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome
Authors: Ai Luoyan , Ren Yimeng , Li Yiting , Chen Haoyan , Qian Yun , Lu Shiyuan , Xu Antao , Ren Linlin , Zhao Shuliang , Chen Zhaofei , Chen Ying‐Xuan , Xu Jie , Fang Jing‐Yuan
Published: December 2018

The molecular mechanisms that control the development of colorectal cancer (CRC) remain poorly defined. Here we show Synbindin promoted CRC oncogenesis by activating Wnt signaling and altering gut microbiome. Synbindin upregulation in human CRCs was associated with poor patient prognosis. Intestine‐specific disruption of Synbindin balanced the disturbed gut microbiota and protected mice against tumor formation in the colitis‐associated cancer (CAC) model. The protective role was compromised after gut microbiota depletion. In host, increased goblet cells and mucin2 expression, together with increased intestinal epithelial cells (IECs) apoptosis and decreased epithelial proliferation were observed. Further transcriptomic sequencing identified Wnt signaling a major regulatory node downstream of Synbindin. Combined molecular and cellular characterizations revealed that Synbindin confers Disheveled‐3 (DVL3)‐based signalosome assembly and acts as a modular scaffold for DVL3 and Axin2 complex, orchestrating the intensity of Wnt signaling. These findings identify a critical role of Synbindin in gut microbiome composition and Wnt signaling activation in colorectal carcinogenesis, and highlight Synbindin as an adaptor protein with multifaceted roles.
Ovarian cancer risk factors by tumor aggressiveness: An analysis from the Ovarian Cancer Cohort Consortium
Authors: Fortner Renée T. , Poole Elizabeth M. , Wentzensen Nicolas A. , Trabert Britton , White Emily , Arslan Alan A. , Patel Alpa V. , Setiawan V. Wendy , Visvanathan Kala , Weiderpass Elisabete , Adami Hans‐Olov , Black Amanda , Bernstein Leslie , Brinton Louise A. , Buring Julie , Clendenen Tess V. , Fournier Agnès , Fraser Gary , Gapstur Susan M. , Gaudet Mia M. , Giles Graham G. , Gram Inger T. , Hartge Patricia , Hoffman‐Bolton Judith , Idahl Annika , Kaaks Rudolf , Kirsh Victoria A. , Knutsen Synnove , Koh Woon‐Puay , Lacey James V. , Lee I‐Min , Lundin Eva , Merritt Melissa A. , Milne Roger L. , Onland‐Moret N. Charlotte , Peters Ulrike , Poynter Jenny N. , Rinaldi Sabina , Robien Kim , Rohan Thomas , Sánchez Maria‐José , Schairer Catherine , Schouten Leo J. , Tjonneland Anne , Townsend Mary K. , Travis Ruth C. , Trichopoulou Antonia , van den Brandt Piet A. , Vineis Paolo , Wilkens Lynne , Wolk Alicja , Yang Hannah P. , Zeleniuch‐Jacquotte Anne , Tworoger Shelley S.
Published: December 2018

Ovarian cancer risk factors differ by histotype; however, within subtype, there is substantial variability in outcomes. We hypothesized that risk factor profiles may influence tumor aggressiveness, defined by time between diagnosis and death, independent of histology. Among 1.3 million women from 21 prospective cohorts, 4,584 invasive epithelial ovarian cancers were identified and classified as highly aggressive (death in <1 year, n = 864), very aggressive (death in 1 to < 3 years, n = 1,390), moderately aggressive (death in 3 to < 5 years, n = 639), and less aggressive (lived 5+ years, n = 1,691). Using competing risks Cox proportional hazards regression, we assessed heterogeneity of associations by tumor aggressiveness for all cases and among serous and endometrioid/clear cell tumors. Associations between parity (phet = 0.01), family history of ovarian cancer (phet = 0.02), body mass index (BMI; phet ≤ 0.04) and smoking (phet < 0.01) and ovarian cancer risk differed by aggressiveness. A first/single pregnancy, relative to nulliparity, was inversely associated with highly aggressive disease (HR: 0.72; 95% CI [0.58–0.88]), no association was observed for subsequent pregnancies (per pregnancy, 0.97 [0.92–1.02]). In contrast, first and subsequent pregnancies were similarly associated with less aggressive disease (0.87 for both). Family history of ovarian cancer was only associated with risk of less aggressive disease (1.94 [1.47–2.55]). High BMI (≥35 vs. 20 to < 25 kg/m2, 1.93 [1.46–2.56] and current smoking (vs. never, 1.30 [1.07–1.57]) were associated with increased risk of highly aggressive disease. Results were similar within histotypes. Ovarian cancer risk factors may be directly associated with subtypes defined by tumor aggressiveness, rather than through differential effects on histology. Studies to assess biological pathways are warranted.
Dynamic temperature changes in wastewater treatment plants
Authors: Scherfig Jan , Schleisner Lotte , Brønd Søren , Kilde Niels
Published: December 2018

Biological treatment processes, especially nitrification and denitrification, are very sensitive to temperature changes lower than 10°C. Short‐term temperature changes occur frequently in many areas of the world, such as Northern Europe. To aid in the design and optimization of treatment plants, a dynamic model has been developed. The model predicts the hourly temperature in biological treatment tanks within 0.5°C over a 1‐month period when the hydraulic residence times range between 12 and 36 hours. Use of the model requires only the initial temperature in the treatment tank, 6‐hour values for the meteorological parameters, and the hourly influent temperature. The major finding is that the temperature variation is very dependent on local wind conditions, which can be modified by windbreaks or (more expensively) by tank covers. The model can be used for quantitative calculations in the design process to minimize temperature drops during cold weather periods and, thus, reduce the required tank volumes.
The Effect of pH, Temperature, and Molecular Size on the Removal of Dyes from Textile Effluent Using Manganese Oxides‐Modified Diatomite
Authors: Khraisheh M. A. M. , Al‐Ghouti M. A. , Allen S. J. , Ahmad M. N. M.
Published: December 2018

This work is an investigation on the use of manganese oxides‐modified diatomite (MOMD) for the removal of color from textile wastewaters. The modification of the diatomite was carried out by treatment with manganese oxides; δ–birnessite type resulted. The surface area, pHZPC, Fourier transform infrared (FTIR), and scanning electron microscopy of MOMD were studied. The influence of concentration, pH, particle size, and temperature on the adsorption capacities of methylene blue (MB) and hydrolyzed reactive black (RB) and reactive yellow (RY) was investigated. Key thermodynamic parameters such asΔHo, ΔSo, and ΔGo were also determined. The ΔHo of MB and hydrolyzed RB and RY was +94.64, −143.1, and −38.78 kJ/mol, respectively, whereas the ΔGo values of −17.68, −27.93, and −23.26 kJ/mol were obtained, indicating a spontaneous process with low activation‐energy requirements. The findings further indicated that coulomb interaction, molecular size, and orientation of the dye and its surface charge played an important role in the adsorption and attachment of the dyes to the birnessite layers of MOMD.
Effect of Alum Addition on the Performance of Submerged Membranes for Wastewater Treatment
Authors: Holbrook R. David , Higgins Matthew J. , Murthy Sudhir N. , Fonseca Anabela D. , Fleischer Edwin J. , Daigger Glen T. , Grizzard Thomas J. , Love Nancy G. , Novak John T.
Published: December 2018

The effect of aluminum sulfate (alum) addition on membrane performance was investigated, with a particular focus on membrane fouling. During initial operation, alum was added and the performance monitored. After terminating alum addition, the transmembrane pressure (TMP), which is indicative of membrane resistance to flow or fouling, increased. Accompanying the increase in TMP was an increase in the organic nonsettleable fraction (colloidal + dissolved) content of the mixed liquor and deterioration of permeate quality and floc strength. Permeate polysaccharide concentrations increased significantly, suggesting a preferential binding of solution polysaccharides by alum. Upon reinitiating alum addition, the TMP only partially recovered, indicating some irreversible fouling, while mixed liquor nonsettleable organic material, permeate quality, and floc strength returned to initial levels. These results suggest that direct alum addition to membrane bioreactors can improve membrane performance by reducing the organic fouling material and improving floc structure and strength. It appears that bulk liquid polysaccharides may contribute to irreversible membrane fouling, and this fraction can be efficiently controlled through the alum addition.
Emerging Pollutants – Part II: Treatment
Authors: Keen Olya S. , Bell Katherine Y. , Cherchi Carla , Finnegan Benjamin J. , Mauter Meagan S. , Parker Austa Marie , Rosenblum James S. , Stretz Holly A.
Published: December 2018

The goal of this review is to summarize new research published in the field of emerging pollutants in the past year. For the purpose of the review, unregulated and relatively new compounds found in wastewater, drinking water, recycled water and the environment were considered. The review consists of two parts, with Part I focusing on the occurrence of the contaminants in the media mentioned above, and Part II focusing on the treatment technologies.
Percutaneous ethanol ablation of intrahepatic arterial pseudoaneurysm: A case report
Authors: Chou Yen , Chou Yi‐Hong , Chiou Yi‐You , Wang Hsin‐Kai , Lai Yi‐Chen , Lin Yung‐Hui , Chiou Hong‐Jen , Tiu Chui‐Mei
Published: December 2018

Hepatic arterial pseudoaneurysm is a rare but potentially fatal condition that requires prompt management. We report a case of hepatic arterial pseudoaneurysm developed after radiofrequency ablation of a hepatocellular carcinoma. The patient was successfully treated with percutaneous absolute ethanol injection under ultrasound guidance. Follow‐up studies with ultrasound and computed tomography for 2 years after treatment revealed no evidence of local recurrence of hepatocellular carcinoma and of the pseudoaneurysm.
Optimal surgical treatment in patients with T1b gallbladder cancer: An international multicenter study
Authors: Kim Hyeong Seok , Park Jae Woo , Kim Hongbeom , Han Youngmin , Kwon Wooil , Kim Sun‐Whe , Hwang Yoon Jin , Kim Sang Geol , Kwon Hyung Jun , Vinuela Eduardo , Járufe Nicolas , Roa Juan Carlos , Han In Woong , Heo Jin Seok , Choi Seong‐Ho , Choi Dong Wook , Ahn Keun Soo , Kang Koo Jeong , Lee Woohyung , Jeong Chi‐Young , Hong Soon‐Chan , Troncoso Andres , Losada Hector , Han Sung‐Sik , Park Sang‐Jae , Yanagimoto Hiroaki , Endo Itaru , Kubota Keiichi , Wakai Toshifumi , Ajiki Tetsuo , Adsay Nazmi Volkan , Jang Jin‐Young
Published: December 2018

Background

There is no consensus on the optimal treatment of T1b gallbladder cancer (GBC) due to the lack of evidence and the difficulty of anatomy and pathological standardization.

Methods

A total of 272 patients with T1b GBC who underwent surgical resection at 14 centers with specialized hepatobiliary‐pancreatic surgeons and pathologists in Korea, Japan, Chile, and the United States were studied. Clinical outcomes including disease‐specific survival (DSS) rates according to the types of surgery were analyzed.

Results

After excluding patients, the 237 qualifying patients consisted of 90 men and 147 women. Simple cholecystectomy (SC) was performed in 116 patients (48.9%) and extended cholecystectomy (EC) in 121 patients (51.1%). The overall 5‐year DSS was 94.6%, and it was similar between SC and EC patients (93.7% vs. 95.5%, P = 0.496). The 5‐year DSS was similar between SC and EC patients in America (82.3% vs. 100.0%, P = 0.249) as well as in Asia (98.6% vs. 95.2%, P = 0.690). The 5‐year DSS also did not differ according to lymph node metastasis (P = 0.688) or tumor location (P = 0.474).

Conclusions

SC showed similar clinical outcomes (including recurrence) and survival outcomes as EC; therefore, EC is not needed for the treatment of T1b GBC.
The myth of the collective unconscious
Authors: Mills Jon
Published: December 2018

This essay challenges the most basic tenet of Jung’s analytical psychology, namely, the existence of the collective unconscious. Despite the fact that there are purported to be universal processes and ontological features of mind throughout all psychoanalytical schools of thought, Jung’s is unique in the history of psychoanalytic ideas for positing a supraordinate, autonomous transpersonal psyche that remains the source, ground, and wellspring from which all unconscious and conscious manifestations derive. This bold claim is analyzed through a close inspection of Jung’s texts that questions the philosophical justification for postulating a supernatural macroanthropos or reified collective mind. Pointing out the problems of agency and fallacies of hypostatization, it is not necessary to evoke a transpersonal cosmogony to explain how universality suffuses individual subjectivity within social collectives. Here we may conclude that the collective unconscious construct is a signifier for the common psychological dynamics and characteristics of shared humanity. In this sense, the myth of the collective unconscious is better understood as a metaphor for a higher abstraction or ideal principle ordained with numinous value.
Suicide and suicide behaviors: A review of transcriptomics and multiomics studies in psychiatric disorders
Authors: Zhou Yi , Lutz Pierre‐Eric , Ibrahim El Chérif , Courtet Philippe , Tzavara Eleni , Turecki Gustavo , Belzeaux Raoul
Published: December 2018

Aberrant gene expression can contribute to brain and nervous system dysfunction that causes many psychiatric illnesses. Here, we review how transcriptomic approaches have deepened our understanding of the neurobiological underpinnings of psychiatric disorders and how they have to the identification of biomarkers for these disorders, with a focus on their relevance to suicide and suicide behaviors. We begin by providing an overview of the genetic, transcriptomic, and epigenetic factors (including non‐coding RNAs) implicated in suicide and their roles in the regulation of gene expression. Then, we highlight the unique benefits and limitations of using either postmortem brain or peripheral tissues in transcriptomic analyses. We examine the current shift from candidate gene to genome‐wide approaches in psychiatric research, which are concurrently emerging with the increased consideration of the Research Domain Criteria (RDoC) framework for classifying mental illnesses. Furthermore, we discuss the use of transcription networks and how they can be integrated into multiomic analyses. Finally, we end by highlighting recent findings of peripheral markers of suicide risk identified through the use of transcriptomic tools. Technological advancements and increased accessibility of these technologies are drastically shaping the current research landscape. We present an overview of the significant changes currently taking place to usher in a new era of psychiatric research.
Inflammation by activated macrophage‐like THP‐1 cells increases human dura mater cell adhesion with alteration of integrin α2β1 and matrix metalloproteinase
Authors: Chong Kyuha , Kwon Woo‐Keun , Kim Joo Han , Park Youn‐Kwan , Yoon Wonki , Kim Jong Hyun , Kwon Taek‐Hyun , Moon Hong Joo
Published: December 2018

This study was designed to investigate (i) extracellular matrix to specify adhesive substrates to human dura mater cell (hDMC); (ii) the alteration on adhesion‐related molecules in hDMC; and (iii) secreted matrix metalloproteinases (MMPs) linked with extracellular matrix remodeling after exposure to inflammation. The hDMC was cultured from human dura mater tissue, and the studies were performed with hDMC after co‐culturing with macrophage like THP‐1 cells (Mϕ). The adhesion of co‐cultured hDMC through collagen I increased 6.4‐fold and through collagen IV increased 5.0‐fold compared with the adhesion of naïve cells (p < 0.001). Integrin subtype α2β1 expression was increased 6.3‐fold (p < 0.001) and α1 expression was decreased 2.0‐fold (p < 0.001) in the co‐cultured cells compared with the naïve cells. Co‐culturing induced significant increases in MMP‐1 (13.9‐fold, p < 0.01), MMP‐3 (7.6‐fold, p < 0.01), and VEGF (VEGF: 3.8‐fold, p < 0.05) expression and decreases in MMP‐9 (0.1‐fold, p < 0.01) compared with the sum of naïve hDMC and Mϕ values. Increased hDMC adhesion under inflammatory conditions is caused by an increased cellular affinity for collagen I and IV mediated by increased hDMC levels of integrin subtype α2β1 and environmental MMP‐1, ‐3 and decreased MMP‐9. Selective integrin subtype α2β1 inhibition assay showed 37.8% and 35.7% reduction in adhesion of co‐cultured hDMC to collagen I (p < 0.001) and IV (p = 0.057), respectively. The present study provides insight into the pathological conditions related to dura mater adhesion in inflammation. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 9999:1–11, 2019.
Sarcopenia Index Is a Simple Objective Screening Tool for Malnutrition in the Critically Ill
Authors: Barreto Erin F. , Kanderi Tejaswi , DiCecco Sara R. , Lopez‐Ruiz Arnaldo , Poyant Janelle O. , Mara Kristin C. , Heimgartner Joy , Gajic Ognjen , Rule Andrew D. , Nystrom Erin M. , Kashani Kianoush B.
Published: December 2018

Background

Reliable and valid tools to screen for malnutrition in the intensive care unit (ICU) remain elusive. The sarcopenia index (SI) [(serum creatinine/serum cystatin C) × 100], could be an inexpensive, objective tool to predict malnutrition. We evaluated the SI as a screening tool for malnutrition in the ICU and compared it with the modified‐NUTRIC score.

Materials and Methods

This was a historical cohort study of ICU patients with stable kidney function admitted to Mayo Clinic ICUs between 2008 and 2015. Malnutrition was defined by the Subjective Global Assessment. Diagnostic performance was evaluated with the area under the receiver operating characteristic curve (AUC) and multivariable logistic regression.

Results

Of the 398 included patients, 181 (45%) had malnutrition, with 34 (9%) scored as severely malnourished. The SI was significantly lower in malnourished patients than in well‐nourished patients (64 ± 27 vs 72 ± 25; P = 0.002), and reductions in SI corresponded to increased malnutrition severity (P = 0.001). As a screening tool, the SI was an indicator of malnutrition risk (AUC 0.61) and performed slightly better than the more complex modified‐NUTRIC score (AUC = 0.57). SI cutoffs of 101 and 43 had >90% sensitivity and >90% specificity, respectively, for the prediction of malnutrition. Patients with a low SI (≤43) had a significantly higher risk of mortality (HR = 2.61, 95% CI 1.06–6.48, P = 0.038).

Conclusion

The frequency of malnutrition was high in this critically ill population, and it was associated with a poor prognosis. The SI could be used to assess nutrition risk in ICU patients.
Beyond Bones: Assessing Whether Ultrasound‐Aided Instruction and Practice Improve Unassisted Soft Tissue Palpation Skills of First‐Year Medical Students
Authors: Walrod Bryant J. , Boucher Laura C. , Conroy Mark J. , McCamey Kendra L. , Hartz Clinton A. , Way David P. , Jonesco Michael A. , Albrechta Steven , Bockbrader Marcia , Bahner David P.
Published: December 2018

Objectives

Our purpose was to determine whether ultrasound (US)‐aided instruction and practice on musculoskeletal anatomy would improve first‐year medical students’ ability to locate and identify specific soft tissue structures by unaided palpation in the upper and lower extremities of healthy human models.

Methods

This study was a randomized crossover design with 49 first‐year medical students randomly assigned to 1 of 2 groups. Each group was provided expert instruction and hands‐on practice using US to scan and study soft tissue structures. During session 1, group A learned the anatomy of the upper extremities, whereas group B learned the lower. Students were then tested on their proficiency in locating 4 soft tissue structures (2 upper and 2 lower extremities) through palpation of a human model. During session 2, group A learned lower extremities, and group B learned upper. At the end of session 2, students repeated the assessment.

Results

After the first instructional session, neither group performed significantly better on identifying and locating the soft tissue landmarks they learned aided by US. After the second instructional session, however, scores for both groups increased approximately 20 percentage points, indicating that both groups performed significantly better on palpating and identifying both the upper and lower extremity soft tissue landmarks (Cohen d = 0.89 and 0.82, respectively).

Conclusions

Time and practice viewing soft tissue structures with US assistance seems to have a “palpation‐with‐eyes” effect that improves students’ abilities to correctly locate, palpate, and identify limb‐specific soft tissue structures once the US assistance is removed.
Exosomes Derived From Low‐Intensity Pulsed Ultrasound‐Treated Dendritic Cells Suppress Tumor Necrosis Factor–Induced Endothelial Inflammation
Authors: Li Xuefeng , Li Xiaoyan , Lin Jing , Sun Xiuyun , Ding Qiuli
Published: December 2018

Objectives

Endothelial cell inflammation plays an important role in atherosclerosis. Low‐intensity pulsed ultrasonography (LIPUS) exerts an anti‐inflammatory function on endothelial cells, whereas the underlying mechanism has not been fully elucidated.

Methods

Bone marrow dendritic cells (BMDCs) derived from bone barrow cells were treated with LIPUS, and exosomes secreted into the supernatant were purified. The isolated exosomes were incubated with human umbilical vein endothelial cells (HUVECs) to investigate their effect on tumor necrosis factor (TNF)‐α–induced endothelial inflammation. Ultrastructure was analyzed by transmission electron microscopy. Messenger RNA levels were determined by quantitative reverse transcription polymerase chain reaction, and protein levels were analyzed by western blot.

Results

The isolated exosomes presented a typical exosomal size of 30 to 100 nm in diameter and expressed exosome positive markers (Alix, CD63, and TSG101) but not the exosome negative marker (Calnexin). Exosomes derived from LIPUS‐treated BMDCs were rich in miR‐16 and miR‐21, which could be engulfed by HUVECs. Pretreatment with exosomes impeded TNFα‐induced HUVEC activation and downregulated TNFα‐stimulated expression of vascular cell adhesion molecule‐1 and intercellular adhesion molecule‐1, thus preventing TNFα‐induced activation of the nuclear factor‐κB signaling pathway.

Conclusion

Exosomes derived from LIPUS‐treated BMDC inhibit TNFα‐induced endothelial inflammation by inhibiting the nuclear factor‐κB signaling pathway.
Allowable take of black vultures in the eastern United States
Authors: Zimmerman Guthrie S. , Millsap Brian A. , Avery Michael L. , Sauer John R. , Runge Michael C. , Richkus Kenneth D.
Published: December 2018

Black vultures (Coragyps atratus) have been increasing in density and expanding their range in the eastern United States since at least the 1960s. In many areas, their densities have increased to the level where they are causing damage to property and livestock and the number of requests for allowable take permits has increased throughout these areas. The United States Fish and Wildlife Service (USFWS) requires updated information to help inform the number of take permits that could reduce conflicts while meeting obligations under the Migratory Bird Treaty Act. We expanded analyses used to estimate allowable take in Virginia to cover the range of black vultures in the eastern United States. We used the prescribed take level approach, which integrates demographic rates, population size estimates, and management objectives into an estimate of allowable take. We provide estimates of allowable take at 4 different scales: individual states, Bird Conservation Regions, USFWS administrative regions, and flyways. Our updated population time series provides evidence of rapidly increasing black vulture populations in many regions of the eastern United States, with an overall population estimate of approximately 4.26 million in 2015 in the Atlantic and Mississippi Flyways. Estimated allowable take ranged from a few hundred individuals per year in states at the northern end of the species range to approximately 287,000/year over the entire eastern United States. The USFWS has no legal mandate regarding the spatial scale at which take should be managed and we found little biological evidence of subpopulation structure for black vultures in the eastern United States. We suggest that allowable take for the species be implemented at a scale that meets stakeholder objectives (e.g., reducing conflict, and ensuring that black vultures are not extirpated from local areas) and is efficient for administrative and monitoring purposes. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
High‐permittivity pad design tool for 7T neuroimaging and 3T body imaging
Authors: van Gemert Jeroen , Brink Wyger , Webb Andrew , Remis Rob
Published: December 2018

Purpose

High‐permittivity materials in the form of flexible “dielectric pads” have proved very useful for addressing RF inhomogeneities in high field MRI systems. Finding the optimal design of such pads is, however, a tedious task, reducing the impact of this technique. We present an easy‐to‐use software tool which allows researchers and clinicians to design dielectric pads efficiently on standard computer systems, for 7T neuroimaging and 3T body imaging applications.

Methods

The tool incorporates advanced computational methods based on field decomposition and model order reduction as a framework to efficiently evaluate the B1+ fields resulting from dielectric pads. The tool further incorporates optimization routines which can either optimize the position of a given dielectric pad, or perform a full parametric design. The optimization procedure can target either a single target field, or perform a sweep to explore the trade‐off between homogeneity and efficiency of the B1+ field in a specific region of interest. The 3T version further allows for shifting of the imaging landmark to enable different imaging targets to be centered in the body coil.

Results

Example design results are shown for imaging the inner ear at 7T and for cardiac imaging at 3T. Computation times for all cases are approximately a minute per target field.

Conclusion

The developed tool can be easily used to design dielectric pads for any 7T neuroimaging and 3T body imaging application within minutes. This bridges the gap between the advanced design methods and the practical application by the MR community.
Population Characteristics and Management of Lentic Populations of Nonnative Burbot in the Green River System, Wyoming
Authors: Brauer Tucker A. , Quist Michael C. , Rhea Darren T. , Laughlin Troy W. , Walrath John D.
Published: December 2018

Fishes introduced outside of their native distributions have the potential to negatively affect their recipient ecosystems. Since their illegal introduction into the Green River, Wyoming, in the 1990s, Burbot Lota lota have been sampled in lotic and lentic environments throughout the Green River system, where they pose a threat to native fishes and valuable sport fisheries. In response to this invasion, managers of the Green River have begun to explore the efficacy of a suppression effort targeting Burbot. We sought to the describe population dynamics of Burbot in the lentic portions (i.e., reservoirs) of the Green River system in comparison with Burbot population dynamics in lotic areas of the Green River. We also sought to evaluate potential management scenarios for a suppression program. Burbot for this study were collected from Fontenelle and Flaming Gorge reservoirs in October and November 2016. Growth rates of Burbot in the lentic portion of the system were higher than those for fish in the Green River. Total annual mortality rates (A) of Burbot were approximately 10% lower in the reservoirs (33%) than in the Green River. Additionally, lentic Burbot matured earlier than lotic Burbot. An age-structured population model indicated that Burbot populations were growing rapidly (population growth rate λ = 1.18) in the study reservoirs. Annual exploitation (μ) of juvenile Burbot would need to reach 7%; the μ of mature Burbot would need to increase to 33% or greater (A ≥ 57%) to effectively suppress Burbot in this system. Sensitivity analysis suggested that mortality of age-1 and age-2 Burbot had the greatest influence on λ. However, due to difficulties in collecting juvenile Burbot in the Green River system, focusing removal efforts on mature individuals may be the most realistic option for suppressing Burbot populations in this system.
Juvenile Salmonid Assemblages at the Mirror Lake Complex in the Lower Columbia River before and after a Culvert Modification
Authors: Sol Sean Y. , Hanson Amanda C. , Marcoe Keith , Johnson Lyndal L.
Published: December 2018

This study examined salmonid assemblages upstream of a culvert connecting the Mirror Lake Complex with the lower Columbia River before and after the culvert was modified to improve habitat connectivity and fish passage. Initially the culvert limited water flow between the Columbia River and the Mirror Lake Complex. The outlet and interior of the culvert were reconfigured to create a more “natural” and suitable passageway for salmonids through the removal of riprap and the strategic placement of boulders, cobbles, gravels, baffles, and weirs. Prior to the culvert modification, three sites were sampled monthly between April and August of 2008, 5.0 and 0.5 km upstream of the culvert and immediately downstream of the culvert. After the culvert modification, the same sites were sampled from 2009 to 2012, with two additional sites added in 2010. Sites near the culvert supported Chinook Salmon Oncorhynchus tshawytscha, Coho Salmon O. kisutch, and Chum Salmon O. keta, while sites further from the culvert supported unmarked Coho Salmon and Rainbow Trout O. mykiss, steelhead (anadromous Rainbow Trout), and Cutthroat Trout O. clarkii. Clear trends in salmonid occurrence were not observed, although densities of Chinook Salmon tended to be higher in years postmodification than before modification. Culvert modifications should focus on alleviating site-specific fish passage conditions to result in substantial changes to habitat connectivity.
Fecal Microbiota Transplantation for the Critically Ill Patient
Authors: Limketkai Berkeley N. , Hendler Steven , Ting Peng‐sheng , Parian Alyssa M.
Published: December 2018

The gut microbiome has been implicated in a diversity of diseases, such as irritable bowel syndrome, inflammatory bowel disease, hepatic steatosis, metabolic syndrome, obesity, and anxiety. Current research also suggests the presence of a bidirectional relationship between the composition of the gut microbiome and critical illness. In the critical care setting, multiple factors (eg, use of antibiotics, aberrant nutrition, bloodstream infections, bowel ischemia, and abnormal bowel motility) strongly contribute to intestinal dysbiosis. Conversely, early studies have associated intestinal dysbiosis with worse clinical outcomes in the intensive care unit (ICU), such as infection, organ failure, and mortality. The possibility of intestinal dysbiosis influencing these clinical outcomes has prompted the question of whether microbiome manipulation strategies, such as fecal microbiota transplantation (FMT), may have a role in the management of critical illness. After a literature search of FMT used in the ICU for indications other than Clostridium difficile infections, we found 4 case reports that describe the use of FMT in 5 critically ill patients with systemic inflammatory responses and no clear source of infection. This review discusses the relationship between the gut microbiome and critical illness, early data on the use of FMT in critical care, and safety considerations of FMT in the critically ill and immunocompromised populations.
Genomic landscape and evolutionary trajectories of ovarian cancer precursor lesions
Authors: Wu Ren‐Chin , Wang Pei , Lin Shiou‐Fu , Zhang Ming , Song Qianqian , Chu Tiffany , Wang Brant G , Kurman Robert J , Vang Russell , Kinzler Kenneth , Tomasetti Cristian , Jiao Yuchen , Shih Ie‐Ming , Wang Tian‐Li
Published: December 2018

The clonal relationship between ovarian high‐grade serous carcinoma (HGSC) and its presumed precursor lesion, serous tubal intraepithelial carcinoma (STIC), has been reported. However, when analyzing patients with concurrent ovarian carcinoma and tubal lesion, the extensive carcinoma tissues present at diagnosis may have effaced the natural habitat of precursor clone(s), obscuring tumor clonal evolutionary history, or may have disseminated to anatomically adjacent fimbriae ends, masquerading as precursor lesions. To circumvent these limitations, we analyzed the genomic landscape of incidental tubal precursor lesions including p53 signature, dormant STIC or serous tubal intraepithelial lesion (STIL) and proliferative STIC in women without ovarian carcinoma or any cancer diagnosis using whole‐exome sequencing and amplicon sequencing. In three of the four cancer‐free women with multiple discrete tubal lesions we observed non‐identical TP53 mutations between precursor lesions from the same individual. In one of the four women with co‐existing ovarian HGSC and tubal precursor lesion we found non‐identical TP53 mutations and a lack of common mutations shared between her precursor lesion and carcinoma. Analyzing the evolutionary history of multiple tubal lesions in the same four patients with concurrent ovarian carcinoma indicated distinct evolution trajectories. Collectively, the results support diverse clonal origins of tubal precursor lesions at the very early stages of tumorigenesis. Mathematical modeling based on lesion‐specific proliferation rates indicated that p53 signature and dormant STIC may take a prolonged time (two decades or more) to develop into STIC, whereas STIC may progress to carcinoma in a much shorter time (6 years). The above findings may have implications for future research aimed at prevention and early detection of ovarian cancer. Copyright © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Patients with cystic fibrosis having a residual function mutation: Data from the Italian registry
Authors: Salvatore Donatello , Padoan Rita , Buzzetti Roberto , Amato Annalisa , Giordani Barbara , Ferrari Gianluca , Majo Fabio
Published: December 2018

Background

CFTR mutations permitting residual function (RF) of the CFTR protein are disease‐causing. These mutations are associated with a pneumopathy that is delayed in onset and is slower in progression than are more common forms of cystic fibrosis (CF), although the disease may become severe in some patients. RF mutations are among the most frequent in Italy, thus encouraging investigation of their prevalence and associated phenotypes.

Methods

Data from the Italian Registry were used to compare patients with at least one RF mutation with those homozygous for F508del.

Results

A total of 806 patients bearing at least one RF mutation were identified among 5204 registered patients (15.5%). The RF patients were older than the F508del homozygotes (median age 26.0 years vs 19.8 years, respectively), with a higher median age at diagnosis (6.3 years vs 0.2 years, respectively) and a lower median sweat chloride value (76.0 mmol/L vs 100.0 mmol/L, respectively). In the RF group, lung infections and comorbidities were less prevalent than those in the F508del homozygotes, while better FEV1 and nutritional status were observed at all ages. Within the RF group, RF/F508del subjects showed more severe pneumopathy than did patients with RF/other mutations. In particular, the 3849 + 10kbC → T/F508del subjects had worse FEV1 and a higher prevalence of lung infections than did patients with other genotypes.

Conclusions

Patients with RF mutations are numerous in Italy and have a milder disease phenotype than do F508del homozygotes. Inside the RF group, F508del heterozygotes and, in particular, 3849 + 10kbC → T/F508del patients showed more severe pneumopathy.
Structural and functional characterization of type three secretion system ATPase PscN and its regulator PscL from Pseudomonas aeruginosa
Authors: Halder Pranab Kumar , Roy Chittran , Datta Saumen
Published: December 2018

Type Three Secretion Systems (T3SS) from many gram‐negative bacteria utilize ATPases for the translocation of effector proteins into the eukaryotic host cells through injectisome. Cytosolic regulators effectively control the action of these ATPases. PscN from Pseudomonas aeruginosa was an ATPase which was regulated by an uncharacterized PscL. Here we have bioinformatically, biochemically, and biophysically characterized PscN as a T3SS ATPase and PscL as its regulator. In solution, PscN exists predominantly as oligomer and hydrolyzes ATP with Vmax of 3.9 ± 0.2 μmol/min/mg and K
m 0.93 ± 0.06 mM. Hexameric structure of PscN was observed under AFM and TEM in the presence of ATP. PscL was dimeric in solution and interacted with PscN strongly in Ni‐NTA pull‐down assay and SPR analysis. PscL was shown to downregulate PscN ATPase activity up to 80% when mixed with PscN in 1:2 ratio (PscN:PscL). SEC data reconfirm the PscN–PscL interaction stoichiometry (ie, 1:2 ratio) which can also be visualized under AFM. In the present study, we have also found out the existence of an oligomeric form of the PscN–PscL heterotrimeric complex. PscL being the regulator of PscN and interacts to form this conformation, which may play an important role too in the regulation of T3SS utilized by Pseudomonas aeruginosa. For structural aspect, three dimensional in silico models of PscN, PscL, and PscN–PscL were generated. So, in short, present study tried to enlighten both the structural, functional and mechanistic insights into the action of PscN–PscL complex in T3SS mediated pathogenic pathway.
Combined Temperature Radiation Effects and Influence of Drawing Conditions on Phosphorous‐Doped Optical Fibers
Authors: Di Francesca Diego , Girard Sylvain , Agnello Simonpietro , Alessi Antonino , Marcandella Claude , Paillet Philippe , Ouerdane Youcef , Kadi Yacine , Brugger Markus , Boukenter Aziz
Published: December 2018

This work focuses on the effects of high dose ionizing radiation, up to 10 MGy(SiO2), on P‐doped multimode optical fibers (OF) at different irradiation temperatures. The investigation is based on two complementary experimental techniques: radiation‐induced attenuation (RIA) measurements and electron paramagnetic resonance (EPR). The latter technique allows measuring the P1, P2, metastable‐POHC and stable‐POHC defects. Three OF samples are drawn from the same preform to evaluate the influence of changing their drawing conditions of the OFs on the radiation responses. This first study is performed under X‐rays at room temperature. The results are compared with the ones of γ‐rays irradiation. The latter allows to highlight a linear correlation between the NIR absorption band at 1.6 µm and the EPR signal of P1 defects, which supports D. Griscom's assignment of this absorption band to the P1 defect. The combined effect of ionizing radiation and irradiation temperature is also investigated extensively: online RIA measurements as well as post‐mortem EPR measurements for irradiation temperatures ranging from 25 to 280 °C and doses up to 3 MGy are performed. Both RIA and EPR data show that increasing the irradiation temperature can lead to an increased production of point defects and associated absorption bands. This result is of great importance for the employment of P‐doped OFs in radiation environment.
Sulfur isotope analysis of microcrystalline iron sulfides using secondary ion mass spectrometry imaging: Extracting local paleo‐environmental information from modern and ancient sediments
Authors: Bryant Roger N. , Jones Clive , Raven Morgan R. , Gomes Maya L. , Berelson William M. , Bradley Alexander S. , Fike David A.
Published: December 2018

Rationale

Sulfur isotope ratio measurements of bulk sulfide from marine sediments have often been used to reconstruct environmental conditions associated with their formation. In situ microscale spot analyses by secondary ion mass spectrometry (SIMS) and laser ablation multiple‐collector inductively coupled plasma mass spectrometry (LA‐MC‐ICP‐MS) have been utilized for the same purpose. However, these techniques are often not suitable for studying small (≤10 μm) grains or for detecting intra‐grain variability.

Methods

Here, we present a method for the physical extraction (using lithium polytungstate heavy liquid) and subsequent sulfur isotope analysis (using SIMS; CAMECA IMS 7f‐GEO) of microcrystalline iron sulfides. SIMS sulfur isotope ratio measurements were made via Cs+ bombardment of raster squares with sides of 20–130 μm, using an electron multiplier (EM) detector to collect counts of 32S− and 34S− for each pixel (128 × 128 pixel grids) for between 20 and 960 cycles.

Results

The extraction procedure did not discernibly alter pyrite grain‐size distributions. The apparent inter‐grain variability in 34S/32S in 1–4 μm‐sized pyrite and marcasite fragments from isotopically homogeneous hydrothermal crystals was ~ ±2‰ (1σ), comparable with the standard error of the mean for individual measurements (≤ ±2‰, 1σ). In contrast, grain‐specific 34S/32S ratios in modern and ancient sedimentary pyrites and marcasites can have inter‐ and intra‐grain variability >60‰. The distributions of intra‐sample isotopic variability are consistent with bulk 34S/32S values.

Conclusions

SIMS analyses of isolated iron sulfide grains yielded distributions that are isotopically representative of bulk 34S/32S values. Populations of iron sulfide grains from sedimentary samples record the evolution of the S‐isotopic composition of pore water sulfide in their S‐isotopic compositions. These data allow past local environmental conditions to be inferred.