bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy Efficiency of the Russian Regional Economy (a case study of the Sverdlovsk Region)
Authors: Teslyuk L , Boyarinov A , Dukmasova N
Published: August 2020

Today, Russia has the second highest value of GDP energy intensity in the world. Among many factors that determine this indicator, special mention can be made of low use efficiency of the fuel and energy resources. This leads to a decreased competitiveness of the national economy. The aim of this paper is to identify practical challenges that serve as a barrier to the reduction of specific energy consumption and to respond with optimal solutions at the level of a territorial entity of Russia (the Sverdlovsk region). The analysis of the fuel and energy balances and the gross regional product between 2015 and 2018 enabled us to identify the changes in the pattern of fuel and energy resources consumption in individual sectors of economy, as well as influencing factors. Special attention is given to the dynamics of average specific energy consumption indicators and to the status of communal infrastructure in the housing and community amenities sector. The study revealed that reduction of technical and commercial losses due to modernization of communal systems and implementation of energy-saving technologies can be achieved through efficient management via further development of public private partnership.
City railways – who are their passengers?
Authors: Pokusaev Oleg , Chekmarev Alexander , Namiot Dmitry
Published: August 2020

In this paper, the approaches to forecasting of passenger flows for new lines of the city railway are analyzed. The article analyzes the experience gained in designing of Moscow central diameters, in the modeling and analysis of their integration with the Moscow Metro and ground urban passenger transport. The main attention is paid to how modern telecommunication technologies make it possible to measure various movements of mobile subscribers, who are passengers, quite accurately. It is the development of telecommunication technologies that is changing the approaches to solving transport problems. What used to be seen as a goal for most transport tasks and was a forecasting goal has now become raw data and can be accurately measured. The article considers what the analysis of transport flows in a modern city now looks like.
Global sustainable development and academic mobility
Authors: Polkovnikova N , Balk M , Panzabekova A , Yarygina A
Published: August 2020

Academic mobility is an important indicator of a country’s competitiveness in innovations and research. Innovations play an important role for sustainable development as defined by UN 2030 goals. In this research we have studied how academic mobility is correlated with national economies.
Assessment of Automobile Transport-related Pollution in Cities at Low Ambient Air Temperatures
Authors: Gavaev Aleksandr S , Ertman Sergei A
Published: August 2020

This article covers a number of issues related to identification of environmental pollution with combustion gas emissions from vehicle engines in urban areas at low ambient air temperatures. Ambient air quality in urban living areas depends on elimination of adverse impact of traffic-related pollution on environmental well-being of citizens. This article gives an overview of dependences of the number of vehicles warmed up at night time and in the morning at ambient air temperatures below zero. Massive emissions subject to ambient air temperature for open air car parking have been determined. It has been established that most of car owners violate the Russian Federation legislation in terms of failure to comply with its bylaw, namely the Traffic Regulations. Based on the results of the conducted study, certain measures have been provided to identify law violators and to strengthen control of compliance with the Traffic Regulations. While discussing the study results a suggestion has been formulated that inevitability of punishment will contribute to raising effectiveness of environmental pollution control in large cities. Cultivation of environmental policy and management system should also be kept in line with up-to-date international needs and requirements and enable effectiveness and efficiency of environmental-related activities in the state.
Natural Factors of Sustainable Development of the Central-Black-Earth District
Authors: Krupko A E , Rogozina R E , Fetisov Yu M , Derevyagina M V , Shentseva L N
Published: August 2020

The article discusses the issues of sustainable development of the region by the example of one of the old-developed economic regions of Russia - Central Black Earth, gives an analysis of the state of natural resources subjected to the active anthropogenic impact, reveals the factors and problems of using the main types of resources, shows the directions for their conservation and possible optimization.
Influence of Technogenic Pollution on the Pigments Concentration in the Black Poplar Leaves (Populus nigra L.) in Biiysk
Authors: Sokolova G G , Khlebova L P , Kalgina M V
Published: August 2020

The article presents the results of a study of the content of pigments in the leaves of black poplar growing along the auto roads in Biysk. The increase in technogenic pollution contributes to the change in the amount and ratio of basic and additional pigments. Compared with the control, a significant decrease in the content of chlorophyll a and the ratio of chlorophyll a/b, a significant increase in the content of chlorophyll b and carotenoids were revealed.
Features of Bioecology of Tree Species Intended for the Implementation of the National Project “Improvement of the Volga” in the Volgograd Region
Authors: Iozus A P , Boyko S Yu , Zavyalov A A
Published: August 2020

Within the framework of the implementation of the national project “Improvement of the Volga”, it is planned to create a system of water protective forest belts along the banks of the Volga River. On the territory of the Volgograd region, forest strips will have to be created on unproductive, saline, gravelly and eroded soils. Therefore, to create plantings, we suggest using planting material selected as a result of many years of selection work, characterized by increased salt tolerance, frost resistance and durability. In extreme soil and climatic conditions of the region, when selecting an assortment of protective forest stands, the additive effect of salinization and drought on tree-shrub vegetation should be taken into account, especially on saline soils of low forest suitability. As a result of the research, it was possible to identify groups of tree species by the degree of increase in salt tolerance, which will allow introducing into the protective forest stands the sustainable and durable species and forms of woody plants created under the project.
Rising to the challenge: Pharmacy residents on the front lines during COVID-19 pandemic
Authors: Uchida Emma , Long-Fazio Bianca , Marshall John , Fortier Christopher
Published: August 2020

Purpose

To provide pharmacy residents’ perspective on how the department of pharmacy at a large academic medical center prepared and managed the surge in admissions of patients with coronavirus disease 2019 (COVID-19), to describe how residents were trained for intensive care unit (ICU) staffing, and to provide recommendations on how residency programs nationally could navigate a second wave of COVID-19 admissions or other disaster response situations.

The majority of postgraduate year 1 (PGY1) pharmacy residents at the institution were trained for ICU staffing and deployed throughout the hospital to ICU units converted to dedicated COVID-19 ICUs to assist in patient care. The training process included live videoconference lectures about relevant ICU topics and on-site experiences with critical care clinical pharmacists. Based on their experience in training for and participating in ICU care of patients with COVID-19, the pharmacy residents recommend considering additional cross-training of residents, integration of additional clinical education, creation of opportunities for resident involvement in telehealth, advancement of residents’ roles in emergency responses, building robust mental health services, and continued advocacy for the advancement of pharmacists’ and pharmacy residents’ scope of practice.

Conclusion

The onset of the COVID-19 pandemic caused the institution to reevaluate the allocation of resources, and the department of pharmacy elected to deploy PGY1 pharmacy residents with previous ICU experience to assist in caring for an ICU patient census that had doubled. This experience will be valuable in preparing for another potential wave of COVID-19 cases and a surge in admissions of other groups of patients who deferred care due to the pandemic.
Evidence of Absence: Bayesian Way to Reveal True Zeros Among Occupational Exposures
Authors: Lavoue Jerome , Burstyn Igor
Published: August 2020

Objectives

Workplace exposure measurements typically contain some observations below limit of detection. The current paradigm for exposure data interpretation relies on the lognormal distribution, where censored observation are assumed to be present but not quantifiable. However, there are setting were such assumptions are untenable and true zero exposures cannot be ruled out. This issue can be non-trivial because decisions about compliance depend on the adequacy of the lognormal model.

Methods

We adapted previously described statistical models for mixture of true zeros and lognormal distribution to function within Bayesian procedure that overcomes historical limitations that precluded them from being used in practice. We compared the performance of the new models and the traditional lognormal model in simulation. Their implementation is illustrated in diverse datasets.

Results

The approach we propose involves estimating the proportion of true zeroes, and the geometric mean and standard deviation of the lognormal component of the mixture. This can be implemented in practice either based on the truncated lognormal model fit to the observed data, or on the censored Bernoulli-lognormal mixture model, which has the advantage of allowing for multiple censoring points. Both models can be implemented via a free online application. In simulations, when none of the censored values were zeros, all estimation procedures led to similar risk assessment. However, when all or most of the censored values were zeros, the traditional approach that assumes lognormal distribution performed noticeably worse than newly proposed methods, typically overestimating noncompliance. Application to real data suggests that we cannot rule out presence of true zero exposures in typical measurement series gathered by occupational hygienists.

Conclusions

Forcing the usual lognormal model to data containing a large proportion of censored values can bias risk assessment if a substantial part of the censored points are true zeroes. The Bernoulli-lognormal model is a suitable and accessible model that can account for such challenging data, and leads to unbiased risk assessments regardless of the presence of true zeros in the data.
Effects of fragmentation of clones compound over vegetative generations in the floating plantPistia stratiotes
Authors: Adomako Michael Opoku , Alpert Peter , Du Dao-Lin , Yu Fei-Hai
Published: August 2020

Background and Aims

Clonal plants dominate many plant communities, especially in aquatic systems, and clonality appears to promote invasiveness and to affect how diversity changes in response to disturbance and resource availability. Understanding how the special physiological and morphological properties of clonal growth lead to these ecological effects depends upon studying the long-term consequences of clonal growth properties across vegetative generations, but this has rarely been done. This study aimed to show how a key clonal property, physiological integration between connected ramets within clones, affects the response of clones to disturbance and resources in an aquatic, invasive, dominant species across multiple generations.

Methods

Single, parental ramets of the floating stoloniferous plant Pistia stratiotes were grown for 3 weeks, during which they produced two or three generations of offspring; connections between new ramets were cut or left intact. Individual offspring were then used as parents in a second 3-week iteration that crossed fragmentation with previous fragmentation in the first iteration. A third iteration yielded eight treatment combinations, zero to three rounds of fragmentation at different times in the past. The experiment was run once at a high and once at a low level of nutrients.

Results

In each iteration, fragmentation increased biomass of the parental ramet, decreased biomass of the offspring and increased number of offspring. These effects persisted and compounded from one iteration to another, though more recent fragmentation had stronger effects, and were stronger at the low than at the high nutrient level. Fragmentation did not affect net accumulation of mass by groups after one iteration but increased it after two iterations at low nutrients, and after three iterations at both nutrient levels.

Conclusions

Both the positive and negative effects of fragmentation on clonal performance can compound and persist over time and can be stronger when resource levels are lower. Even when fragmentation has no short-term net effect on clonal performance, it can have a longer-term effect. In some cases, fragmentation may increase total accumulation of mass by a clone. The results provide the first demonstration of how physiological integration in clonal plants can affect fitness across generations and suggest that increased disturbance may promote invasion of introduced clonal species via effects on integration, perhaps especially at lower nutrient levels.
Publishing reproducible dynamic kinetic models
Authors: Porubsky Veronica , Smith Lucian , Sauro Herbert M
Published: August 2020

Publishing repeatable and reproducible computational models is a crucial aspect of the scientific method in computational biology and one that is often forgotten in the rush to publish. The pressures of academic life and the lack of any reward system at institutions, granting agencies and journals means that publishing reproducible science is often either non-existent or, at best, presented in the form of an incomplete description. In the article, we will focus on repeatability and reproducibility in the systems biology field where a great many published models cannot be reproduced and in many cases even repeated. This review describes the current landscape of software tooling, model repositories, model standards and best practices for publishing repeatable and reproducible kinetic models. The review also discusses possible future remedies including working more closely with journals to help reviewers and editors ensure that published kinetic models are at minimum, repeatable. Contact: hsauro@uw.edu
In utero low-protein-diet-programmed type 2 diabetes in adult offspring is mediated by sex hormones in rats†
Authors: Blesson Chellakkan S , Schutt Amy K , Vipin Vidyadharan A , Tanchico Daren T , Mathew Pretty R , Balakrishnan Meena , Betancourt Ancizar , Yallampalli Chandra
Published: August 2020

Sex steroids regulate insulin sensitivity and glucose metabolism. We had characterized a lean type 2 diabetes (T2D) rat model using gestational low-protein (LP) diet programming. Our objective was to identify if endocrine dysfunction leading to decreased sex hormone levels will precede the development of T2D and if steroid replacement will prevent the onset of the disease. Pregnant rats were fed control or isocaloric LP diet from gestational day 4 until delivery. Normal diet was given to all mothers after delivery and to pups after weaning. LP offspring developed glucose intolerance and insulin resistance at 4 months. We measured sex steroid hormone profiles and expression of key genes involved in steroidogenesis in testis and ovary. Furthermore, one-month old rats were implanted with 90-day slow release T and E2 pellets for males and females, respectively. Glucose tolerance test (GTT) and euglycemic hyperinsulinemic clamp was performed at 4 months. LP-programmed T2D males had low T levels and females had low E2 levels due to dysregulated gene expression during steroidogenesis in gonads. GTT and euglycemic hyperinsulinemic clamp showed that LP males and females were glucose intolerant and insulin resistant; however, steroid supplementation prevented the onset of glucose intolerance and insulin resistance. Rats that developed T2D by LP programming have compromised gonadal steroidogenesis leading to low T and E2 in males and females, respectively. Sex steroid supplementation prevented the onset of glucose intolerance and insulin resistance indicating low sex steroid levels could cause compromised glucose metabolism ultimately leading to T2D.
The enigmatic sperm proteins in mammalian fertilization: an overview†
Authors: Gahlay Gagandeep Kaur , Rajput Neha
Published: August 2020

Mammalian fertilization involves a physical interaction between a sperm and an egg followed by molecular interactions amongst their various cell surface molecules. These interactions are initially mediated on the egg’s outermost matrix, zona pellucida (ZP), and then its plasma membrane. To better understand this process, it is pertinent to find the corresponding molecules on sperm that interact with ZP or the egg’s plasma membrane. Although currently, we have some knowledge about the binding partners for egg’s plasma membrane on sperm, yet the ones involved in an interaction with ZP have remained remarkably elusive. This review provides comprehensive knowledge about the various sperm proteins participating in mammalian fertilization and discusses the possible reasons for not being able to identify the strong sperm surface candidate (s) for ZP adhesion. It also hypothesizes the existence of a multi-protein complex(s), members of which participate in oviduct transport, cumulus penetration, zona adhesion, and adhesion/fusion with the egg’s plasma membrane; with some protein(s) having multiple roles during this process. Identification of these proteins is crucial as it improves our understanding of the process and allows us to successfully treat infertility, develop contraceptives, and improve artificial reproductive technologies.
Effects of Amygdala Lesions on Object-Based Versus Action-Based Learning in Macaques
Authors: Taswell Craig A , Costa Vincent D , Basile Benjamin M , Pujara Maia S , Jones Breonda , Manem Nihita , Murray Elisabeth A , Averbeck Bruno B
Published: August 2020

The neural systems that underlie reinforcement learning (RL) allow animals to adapt to changes in their environment. In the present study, we examined the hypothesis that the amygdala would have a preferential role in learning the values of visual objects. We compared a group of monkeys (Macaca mulatta) with amygdala lesions to a group of unoperated controls on a two-armed bandit reversal learning task. The task had two conditions. In the What condition, the animals had to learn to select a visual object, independent of its location. And in the Where condition, the animals had to learn to saccade to a location, independent of the object at the location. In both conditions choice-outcome mappings reversed in the middle of the block. We found that monkeys with amygdala lesions had learning deficits in both conditions. Monkeys with amygdala lesions did not have deficits in learning to reverse choice-outcome mappings. Rather, amygdala lesions caused the monkeys to become overly sensitive to negative feedback which impaired their ability to consistently select the more highly valued action or object. These results imply that the amygdala is generally necessary for RL.
On-Line Sorbentless Cryogenic Needle Trap and GC–FID Method for the Extraction and Analysis of Trace Volatile Organic Compounds from Soil Samples
Authors: Djozan Djavanshir , Norouzi Jamal , Farajzadeh Mir Ali
Published: August 2020

In this study, an automated sorbentless cryogenic needle trap device (ASCNTD) coupled with a gas chromatograph (GC) was developed with the aim of sampling, pre-concentration and determination of volatile organic compounds (VOCs) from soil sample. This paper describes optimization of relevant parameters, performance evaluation and an illustrative application of ASCNTD. The ASCNTD system consists of a 5 cm stainless steel needle passed through a hollow ceramic rod which is coiled with resistive nichrome wire. The set is placed in a PVC (Polyvinyl chloride) chamber through which liquid nitrogen can flow. The headspace components are circulated with a pump to pass through the needle, and this results in freeze-trapping of the VOCs on the inner surface of the needle. When extraction is completed, the analytes trapped in the inner wall of the needle were thermally desorbed and swept by the carrier gas into the GC capillary column. The parameters being effective on the extraction processes, namely headspace flow rate, the temperature and time of extraction and desorption were optimized and evaluated. The developed technique was compared to the headspace solid-phase microextraction method for the analysis of soil samples containing BTEX (Benzene, Toluene, Ethylbenzene and Xylene). The relative standard deviation values are below 8% and detection limits as low as 1.2 ng g−1 were obtained for BTEX by ASCNTD.
Esophageal cancer surgery in Greece during the era of the financial crisis
Authors: Schizas Dimitrios , Mylonas Konstantinos S , Hasemaki Natasha , Mpaili Efstratia , Ntomi Vasileia , Michalinos Adamantios , Theochari Nikoletta A , Theochari Christina A , Mpoura Maria , Bakopoulos Anargyros , Liakakos Theodoros
Published: August 2020

The aim of this study is to describe outcomes of esophageal cancer surgery in a quaternary upper gastrointestinal (GI) center in Athens during the era of the Greek financial crisis. We performed a retrospective analysis of patients that underwent esophagectomy for esophageal or gastroesophageal junction (GEJ) cancer at an upper GI unit of the University of Athens, during the period January 2004–June 2019. Time-to-event analyses were performed to explore trends in survival and recurrence. A total of 146 patients were identified. Nearly half of the patients (49.3%) underwent surgery during the last 4 years of the financial crisis (2015–2018). Mean age at the time of surgery was 62.3 ± 10.3 years, and patients did not present at older ages during the recession (P = 0.50). Most patients were stage III at the time of surgery both prior to the recession (35%) and during the financial crisis (39.8%, P = 0.17). Ivor–Lewis was the most commonly performed procedure (67.1%) across all eras (P = 0.06). Gastric conduit was the most common form of GI reconstruction (95.9%) following all types of surgery (P < 0.001). Pre-recession anastomoses were usually performed using a circular stapler (65%). Both during (88.1%) and following the recession (100%), the vast majority of anastomoses were hand-sewn. R0 resection was achieved in 142 (97.9%) patients. Anastomosis technique did not affect postoperative leak (P = 0.3) or morbidity rates (P = 0.1). Morbidity rates were not significantly different prior to (25%), during (46.9%), and after (62.5%) the financial crisis, P = 0.16. Utilization of neoadjuvant chemotherapy (26.9%, P = 0.90) or radiation (8.4%, P = 0.44) as well as adjuvant chemotherapy (54.8%, P = 0.85) and irradiation (13.7%, P = 0.49) was the same across all eras. Disease-free survival (DFS) and all-cause mortality rates were 41.2 and 47.3%, respectively. Median DFS and observed survival (OS) were 11.3 and 22.7 months, respectively. The financial crisis did not influence relapse (P = 0.17) and survival rates (P = 0.91). The establishment of capital controls also had no impact on recurrence (P = 0.18) and survival (P = 0.94). Austerity measures during the Greek financial crisis did not influence long-term esophageal cancer outcomes. Therefore, achieving international standards in esophagectomy may be possible in resource-limited countries when centralizing care.
Solute Carrier Family 12 Member 2 as a Proteomic and Histological Biomarker of Dysplasia and Neoplasia in Ulcerative Colitis
Authors: Merli Angela-Maria , Vieujean Sophie , Massot Charlotte , Blétard Noella , Quesada Calvo Florence , Baiwir Dominique , Mazzucchelli Gabriel , Servais Laurence , Wéra Odile , Oury Cécile , de Leval Laurence , Sempoux Christine , Manzini Roberto , Bluemel Sena , Scharl Michael , Rogler Gerhard , De Pauw Edwin , Coimbra Marques C , Colard Arnaud , Vijverman Anne , Delvenne Philippe , Louis Edouard , Meuwis Marie-Alice
Published: August 2020

Background and Aims

Ulcerative colitis [UC] patients have a greater risk of developing colorectal cancer through inflammation-dysplasia-carcinoma sequence of transformation. The histopathological diagnosis of dysplasia is therefore of critical clinical relevance, but dysplasia may be difficult to distinguish from inflammatory changes.

Methods

A proteomic pilot study on five UC colorectal dysplastic patients highlighted proteins differentially distributed between paired dysplastic, inflammatory, and normal tissues. The best candidate marker was selected and immunohistochemistry confirmation was performed on azoxymethane/dextran sulphate sodium [AOM/DSS] mouse model lesions, 37 UC-dysplasias, 14 UC-cancers, 23 cases of long-standing UC, 35 sporadic conventional adenomas, 57 sporadic serrated lesions, and 82 sporadic colorectal cancers.

Results

Differential proteomics found 11 proteins significantly more abundant in dysplasia compared with inflammation, including Solute carrier family 12 member 2 [SLC12A2] which was confidently identified with eight specific peptides and was below the limit of quantitation in both inflammatory and normal colon. SLC12A2 immunohistochemical analysis confirmed the discrimination of preneoplastic and neoplastic lesions from inflammatory lesions in mice, in UC, and in sporadic contexts. A specific SLC12A2 staining pattern termed ‘loss of gradient’ reached 89% sensitivity, 95% specificity, and 92% accuracy for UC-dysplasia diagnosis together with an inter-observer agreement of 95.24% [multirater κ free of 0.90; 95% CI: 0.78 - 1.00]. Such discrimination could not be obtained by Ki67 staining. This specific pattern was also associated with sporadic colorectal adenomas and cancers.

Conclusions

We found a specific SLC12A2 immunohistochemical staining pattern in precancerous and cancerous colonic UC lesions which could be helpful for diagnosing dysplasia and cancer in UC and non-UC patients.
General practitioners’ perspectives of the integrated health care system: a cross-sectional study in Wuhan, China
Authors: Chen Fan , Jiang Qingqing , Lu Zuxun , Cao Shiyi
Published: August 2020

Background

In recent years, the Chinese government has introduced a new system called the integrated health care system to deepen health care reform and enhance the capacity of the primary health care services.

Objective

We aimed to investigate the perceptions and opinions of general practitioners (GPs) on the integrated health care system.

Methods

A cross-sectional investigation involving 764 GPs in Hubei province of China was conducted. We used a self-designed questionnaire to collect information on demographics, GPs’ knowledge and attitude of the integrated health care system. Data on 749 GPs with completed questionnaires were analysed descriptively. We conducted Spearman rank correlation analysis to test correlation of grade data.

Results

60.92% of the 749 GPs were familiar with the integrated health care system. 88.25% of the GPs were apt to support its development and 70.09% thought it could promote downward referral of patients. The GPs’ familiarity with the integrated health care system was significantly related to professional guidance from doctors in higher hospitals (P < 0.05), but not job titles of GPs (P > 0.05). 78.0% of GPs thought that the main benefit of the integrated health care system was the reduction of patients’ health care costs; 70.1% believed that the most difficulty was insufficient publicity.

Conclusions

The GPs’ general cognition of the integrated health care system was general. Most of the GPs supported the integrated health care system and believed that it contributed to decrease the patients’ health care costs. Insufficient publicity and the incomplete two-way referral mechanism were regarded to be the main obstacles to its development.
Cell envelope proteases and peptidases of Pseudomonas aeruginosa: multiple roles, multiple mechanisms
Authors: Heywood Astra , Lamont Iain L
Published: August 2020

Pseudomonas aeruginosa is a Gram-negative bacterium that is commonly isolated from damp environments. It is also a major opportunistic pathogen, causing a wide range of problematic infections. The cell envelope of P. aeruginosa, comprising the cytoplasmic membrane, periplasmic space, peptidoglycan layer and outer membrane, is critical to the bacteria's ability to adapt and thrive in a wide range of environments. Over 40 proteases and peptidases are located in the P. aeruginosa cell envelope. These enzymes play many crucial roles. They are required for protein secretion out of the cytoplasm to the periplasm, outer membrane, cell surface or the environment; for protein quality control and removal of misfolded proteins; for controlling gene expression, allowing adaptation to environmental changes; for modification and remodelling of peptidoglycan; and for metabolism of small molecules. The key roles of cell envelope proteases in ensuring normal cell functioning have prompted the development of inhibitors targeting some of these enzymes as potential new anti-Pseudomonas therapies. In this review, we summarise the current state of knowledge across the breadth of P. aeruginosa cell envelope proteases and peptidases, with an emphasis on recent findings, and highlight likely future directions in their study.
Multi-“-Omics” Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse
Authors: Borren Nienke Z , Plichta Damian , Joshi Amit D , Bonilla Gracia , Sadreyev Ruslan , Vlamakis Hera , Xavier Ramnik J , Ananthakrishnan Ashwin N
Published: August 2020

Background

Inflammatory bowel diseases (IBD) are characterized by intermittent relapses, and their course is heterogeneous and unpredictable. Our aim was to determine the ability of protein, metabolite, or microbial biomarkers to predict relapse in patients with quiescent disease.

Methods

This prospective study enrolled patients with quiescent Crohn disease and ulcerative colitis, defined as the absence of clinical symptoms (Harvey-Bradshaw Index ≤ 4, Simple Clinical Colitis Activity Index ≤ 2) and endoscopic remission within the prior year. The primary outcome was relapse within 2 years, defined as symptomatic worsening accompanied by elevated inflammatory markers resulting in a change in therapy or IBD-related hospitalization or surgery. Biomarkers were tested in a derivation cohort, and their performance was examined in an independent validation cohort.

Results

Our prospective cohort study included 164 patients with IBD (108 with Crohn disease, 56 with ulcerative colitis). Upon follow-up for a median of 1 year, 22 patients (13.4%) experienced a relapse. Three protein biomarkers (interleukin-10, glial cell line–derived neurotrophic factor, and T-cell surface glycoprotein CD8 alpha chain) and 4 metabolomic markers (propionyl-L-carnitine, carnitine, sarcosine, and sorbitol) were associated with relapse in multivariable models. Proteomic and metabolomic risk scores independently predicted relapse with a combined area under the curve of 0.83. A high proteomic risk score (odds ratio = 9.11; 95% confidence interval, 1.90-43.61) or metabolomic risk score (odds ratio = 5.79; 95% confidence interval, 1.24-27.11) independently predicted a higher risk of relapse over 2 years. Fecal metagenomics showed an increased abundance of Proteobacteria (P = 0.0019, q = 0.019) and Fusobacteria (P = 0.0040, q = 0.020) and at the species level Lachnospiraceae_bacterium_2_1_58FAA (P = 0.000008, q = 0.0009) among the relapses.

Conclusions

Proteomic, metabolomic, and microbial biomarkers identify a proinflammatory state in quiescent IBD that predisposes to clinical relapse.
A new tool for discovering transcriptional regulators of co-expressed genes predicts gene regulatory networks that mediate ethylene-controlled root development
Authors: Harkey Alexandria F , Sims Kira N , Muday Gloria K
Published: August 2020

Gene regulatory networks (GRNs) are defined by a cascade of transcriptional events by which signals, such as hormones or environmental cues, change development. To understand these networks, it is necessary to link specific transcription factors (TFs) to the downstream gene targets whose expression they regulate. Although multiple methods provide information on the targets of a single TF, moving from groups of co-expressed genes to the TF that controls them is more difficult. To facilitate this bottom-up approach, we have developed a web application named TF DEACoN. This application uses a publicly available Arabidopsis thaliana DNA Affinity Purification (DAP-Seq) data set to search for TFs that show enriched binding to groups of co-regulated genes. We used TF DEACoN to examine groups of transcripts regulated by treatment with the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), using a transcriptional data set performed with high temporal resolution. We demonstrate the utility of this application when co-regulated genes are divided by timing of response or cell-type-specific information, which provides more information on TF/target relationships than when less defined and larger groups of co-regulated genes are used. This approach predicted TFs that may participate in ethylene-modulated root development including the TF NAM (NO APICAL MERISTEM). We used a genetic approach to show that a mutation in NAM reduces the negative regulation of lateral root development by ACC. The combination of filtering and TF DEACoN used here can be applied to any group of co-regulated genes to predict GRNs that control coordinated transcriptional responses.
ASAS-NANP SYMPOSIUM: RUMINANT/NONRUMINANT FEED COMPOSITION: Challenges and opportunities associated with creating large feed composition tables
Authors: Schlageter-Tello Andres , Fahey George C , Freel Tarra , Koutsos Liz , Miller Phillip S , Weiss William P
Published: August 2020

Traditional feed composition tables have been a useful tool in the field of animal nutrition throughout the last 70 yr. The objective of this paper is to discuss the challenges and opportunities associated with creating large feed ingredient composition tables. This manuscript will focus on three topics discussed during the National Animal Nutrition Program (NANP) Symposium in ruminant and nonruminant nutrition carried out at the American Society of Animal Science Annual Meeting in Austin, TX, on July 11, 2019, namely: 1) Using large datasets in feed composition tables and the importance of standard deviation in nutrient composition as well as different methods to obtain accurate standard deviation values, 2) Discussing the importance of fiber in animal nutrition and the evaluation of different methods to estimate fiber content of feeds, and 3) Description of novel feed sources, such as insects, algae, and single-cell protein, and challenges associated with the inclusion of such feeds in feed composition tables. Development of feed composition tables presents important challenges. For instance, large datasets provided by different sources tend to have errors and misclassifications. In addition, data are in different file formats, data structures, and feed classifications. Managing such large databases requires computers with high processing power and software that are also able to run automated procedures to consolidate files, to screen out outlying observations, and to detect misclassified records. Complex algorithms are necessary to identify misclassified samples and outliers aimed to obtain accurate nutrient composition values. Fiber is an important nutrient for both monogastrics and ruminants. Currently, there are several methods available to estimate the fiber content of feeds. However, many of them do not estimate fiber accurately. Total dietary fiber should be used as the standard method to estimate fiber concentrations in feeds. Finally, novel feed sources are a viable option to replace traditional feed sources from a nutritional perspective, but the large variation in nutrient composition among batches makes it difficult to provide reliable nutrient information to be tabulated. Further communication and cooperation among different stakeholders in the animal industry are required to produce reliable data on the nutrient composition to be published in feed composition tables.
Ultrastructure of the Antennae and Sensilla ofNyssomyia intermedia(Diptera: Psychodidae), Vector of American Cutaneous Leishmaniasis
Authors: Fernandes Fernando de Freitas , Barletta Ana Beatriz F , Orfanó Alessandra S , Pinto Luciana C , Nacif-Pimenta Rafael , Miranda Jose Carlos , Secundino Nágila F C , Bahia Ana Cristina , Pimenta Paulo F P
Published: August 2020

The antennal sensilla and the antenna of females Nyssomyia intermedia, one of the main vectors of American cutaneous leishmaniasis, were studied by scanning electron microscopy. The main goal was to characterize the quantity, typology, and topography of the sensilla with particular attention to the olfactory types. The insects were captured in the city of Corte de Pedra, State of Bahia, Brazil, by CDC-type light traps and raised in a laboratory as a new colony. Fourteen well-differentiated sensilla were identified, among six cuticular types: trichoidea, campaniformia, squamiformia, basiconica, chaetica, and coeloconica. Of these, six sensilla were classified as olfactory sensilla due to their specific morphological features. Smaller noninnervated pilosities of microtrichiae type were also evidenced by covering all antennal segments. The antennal segments differ in shapes and sizes, and the amount and distribution of types and subtypes of sensilla. This study may foment future taxonomic and phylogenetic analysis for a better evolutionary understanding of the sand flies. Besides, it may assist the targeting of future electrophysiological studies by Single Sensillum Recording, and aim to develop alternative measures of monitoring and control of this vector.
The Role of Liquid Biopsies in Pediatric Brain Tumors
Authors: Tang Karen , Gardner Sharon , Snuderl Matija
Published: August 2020

Early detection and serial therapeutic monitoring for pediatric brain tumors are essential for diagnosis and therapeutic intervention. Currently, neuropathological diagnosis relies on biopsy of tumor tissue and surgical intervention. There is a great clinical need for less invasive methods to molecularly characterize the tumor and allow for more reliable monitoring of patients during treatment and to identify patients that might potentially benefit from targeted therapies, particularly in the setting where diagnostic tissue cannot be safely obtained. In this literature review, we highlight recent studies that describe the use of circulating tumor DNA, circulating tumor cells, circulating RNA and microRNA, and extracellular vesicles as strategies to develop liquid biopsies in pediatric central nervous system tumors. Liquid biomarkers have been demonstrated using plasma, urine, and cerebrospinal fluid. The use of liquid biopsies to help guide diagnosis, determine treatment response, and analyze mechanisms of treatment resistance is foreseeable in the future. Continued efforts to improve signal detection and standardize liquid biopsy procedures are needed for clinical application.
Stable Plasma Sample Storage in Acetonitrile for Angiotensin and Aldosterone Analysis
Authors: Wei Xuefei , Wang Yanyang , Zhu Wenbo , Li Jingjing , Peng Lu , Gao Zhiwei , Bai Bing
Published: August 2020

Background

Angiotensin I, II (AI, AII) and aldosterone are unstable in plasma specimens at room temperature, making it difficult for collect samples for remote regions in centralized and collaborative studies. Here we introduce a stable storage method which do not require cold conditions..

Methods

Acetonitrile was added to the plasma to 60%, and then the supernatants were kept at 4°C and room temperature for 0, 1, 2, 3, 10 and 30 days. AI, AII and aldosterone were extracted and analyzed by chemiluminescence immunoassays.

Results

AI, AII and aldosterone were well retained in the supernatant under this method. The intra- and inter-day CVs of this method were all below 10%. The levels of AI, AII and aldosterone by this method remained stable for 30 days at room temperature.

Conclusion

Addition of 60% acetonitrile in the plasma provides a stable storage method for clinical AI, AII and aldosterone.
The impact of stellar and AGN feedback on halo-scale baryonic and dark matter accretion in the eagle simulations
Authors: Wright Ruby J , Lagos Claudia del P , Power Chris , Mitchell Peter D
Published: August 2020

We use the eagle suite of hydrodynamical simulations to analyse accretion rates (and the breakdown of their constituent channels) on to haloes over cosmic time, comparing the behaviour of baryons and dark matter (DM). We also investigate the influence of sub-grid baryon physics on halo-scale inflow, specifically the consequences of modelling radiative cooling, as well as feedback from stars and active galactic nuclei (AGNs). We find that variations in halo baryon fractions at fixed mass (particularly their circumgalactic medium gas content) are very well correlated with variations in the baryon fraction of accreting matter, which we show to be heavily suppressed by stellar feedback in low-mass haloes, Mhalo ≲ 1011.5 M⊙. Breaking down accretion rates into first infall, recycled, transfer, and merger components, we show that baryons are much more likely to be smoothly accreted than to have originated from mergers when compared to DM, finding (averaged across halo mass) a merger contribution of $\approx 6{{\ \rm per\ cent}}$ for baryons, and $\approx 15{{\ \rm per\ cent}}$ for DM at z ≈ 0. We also show that the breakdown of inflow into different channels is strongly dependent on sub-grid physics, particularly the contribution of recycled accretion (accreting matter that has been previously ejected from progenitor haloes). Our findings highlight the dual role that baryonic feedback plays in regulating the evolution of galaxies and haloes: by (i) directly removing gas from haloes, and (ii) suppressing gas inflow to haloes.
Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions
Authors: Campitelli Paul , Swint-Kruse Liskin , Ozkan S Banu
Published: August 2020

Amino acid substitutions at nonconserved protein positions can have noncanonical and “long-distance” outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions (“toggle”), ten nonconserved positions showed progressive changes from a range of substitutions (“rheostat”), and three nonconserved positions tolerated almost all substitutions (“neutral”). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.
hnRNPK recognition of the B motif of Xist and other biological RNAs
Authors: Nakamoto Meagan Y , Lammer Nickolaus C , Batey Robert T , Wuttke Deborah S
Published: August 2020

Heterogeneous nuclear ribonuclear protein K (hnRNPK) is an abundant RNA-binding protein crucial for a wide variety of biological processes. While its binding preference for multi-cytosine-patch (C-patch) containing RNA is well documented, examination of binding to known cellular targets that contain C-patches reveals an unexpected breadth of binding affinities. Analysis of in-cell crosslinking data reinforces the notion that simple C-patch preference is not fully predictive of hnRNPK localization within transcripts. The individual RNA-binding domains of hnRNPK work together to interact with RNA tightly, with the KH3 domain being neither necessary nor sufficient for binding. Rather, the RG/RGG domain is implicated in providing essential contributions to RNA-binding, but not DNA-binding, affinity. hnRNPK is essential for X chromosome inactivation, where it interacts with Xist RNA specifically through the Xist B-repeat region. We use this interaction with an RNA motif derived from this B-repeat region to determine the RNA-structure dependence of C-patch recognition. While the location preferences of hnRNPK for C-patches are conformationally restricted within the hairpin, these structural constraints are relieved in the absence of RNA secondary structure. Together, these results illustrate how this multi-domain protein's ability to accommodate and yet discriminate between diverse cellular RNAs allows for its broad cellular functions.
The AKP’s Rhetoric of Rule in TurkeyPolitical Melodramas of Conspiracy from “Ergenekon” to “Mastermind”
Authors: Göknar Erdağ
Published: August 2020

In 2008 the Turkish Constitutional Court was one vote shy of banning the ruling AKP for “anti-secular activity.” In response, the AKP began articulating a series of political conspiracy narratives, amplified through the media. Blurring the line between representation and reality, these political melodramas set the stage for the exercise of state power through the weaponization of investigations and judicial retaliation against the military and the opposition. From 2008 to 2013, the “Ergenekon” conspiracy depicted an anti-Islamist deep state organization and its involvement in illegal activities including military coups and assassinations—as if it actually existed. The Ergenekon conspiracy (and attendant trials) initiated a profound change in Turkish politics by breaking the power of the traditional secular-military alliance. In 2014, Ergenekon led to a spin-off called “Mastermind”, which targeted the AKP’s erstwhile ally and political rival the Gülen Hizmet (or “Service”) Movement, a transnational Islamic educational and media network led by imam Fetullah Gülen. Gülenists, with their strong presence in the police and judiciary, had been instrumental in the Ergenekon prosecutions. Mastermind was later credited with the anti-AKP Gezi protests and a corruption investigation into then Prime Minister Erdoğan in 2013 as well as for the 2016 failed coup. Relying on a literary-cultural analysis of the political field, this chapter argues that conspiracism in Turkey has functioned to prefigure and legitimate authoritarian governance, whether secular or Islamist. I redefine conspiracy theories as popular fictions indexed to political movements that can instrumentalize legal and electoral processes for the accumulation of state power and the undermining of democratic pluralism.