bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictions, Pivots, and a Pandemic: a Review of 2020's Top Translational Bioinformatics Publications
Authors: McGrath Scott P. , Benton Mary Lauren , Tavakoli Maryam , Tatonetti Nicholas P. 
Published: September 2021

Summary
Objectives: Provide an overview of the emerging themes and notable papers which were published in 2020 in the field of Bioinformatics and Translational Informatics (BTI) for the International Medical Informatics Association Yearbook.
Methods: A team of 16 individuals scanned the literature from the past year. Using a scoring rubric, papers were evaluated on their novelty, importance, and objective quality. 1,224 Medical Subject Headings (MeSH) terms extracted from these papers were used to identify themes and research focuses. The authors then used the scoring results to select notable papers and trends presented in this manuscript.
Results: The search phase identified 263 potential papers and central themes of coronavirus disease 2019 (COVID-19), machine learning, and bioinformatics were examined in greater detail.
Conclusions: When addressing a once in a centruy pandemic, scientists worldwide answered the call, with informaticians playing a critical role. Productivity and innovations reached new heights in both TBI and science, but significant research gaps remain.
Immunofluorescence in Robotic Colon and Rectal Surgery
Authors: Bobel Matthew C. , Altman Ariella , Gaertner Wolfgang B. 
Published: September 2021

AbstractThe indocyanine green fluorescence imaging system is a surgical tool with increasing applications in colon and rectal surgery that has received growing acceptance in various surgical disciplines as a potentially valid method to enhance surgical field visualization, improve lymph node retrieval, and decrease anastomotic leak. Small noncomparative prospective trials have shown that intraoperative fluorescence imaging is a safe and feasible method to assess anastomotic perfusion and that its use may impact anastomotic leak rates. However, larger prospective and randomized studies are required to validate its role and impact in colorectal surgery. The purpose of this article is to review the current status of the use of immunofluorescence in colon and rectal surgery, as well as new applications in robotic colon and rectal resections.
Significance of Detecting Minimal Residual Disease by Flow Cytometry and its Impact on Overall Survival and Prognosis of Pediatric B-Cell ALL Patient Experience from a Tertiary Care Centre in Eastern India
Authors: Mukherjee Kalyan K. , Banerjee Debasish , Das Anjan , Halder Subham , Mukherjee Dattatreya , Mondal Shyam S. , Roy Surya K. , Das Mili , Panda Chinmay K. , Chaudhuri Utpal 
Published: September 2021

Abstract
Introduction The improved prognosis of pediatric B-cell acute lymphoblastic leukemia (pBALL) is considered as a good progress of medical science in the field of oncology and hematology. Minimal residual disease (MRD) refers to presence of disease in molecular level is a newer practice with respect to the detection of complete remission by conventional pathologic analysis. Prognostic value of MRD in pediatric ALL (p-ALL) is well known.
Objectives This study was aimed to describe clinical outcomes and prognosis, that is, overall survival and relapse in the patients with pBALL with respect to minimal residual disease detection on day 15, day 29, and postconsolidations in a tertiary care center in eastern India.
Materials and Methods Eight color flow cytometry was used to detect MRD in this study. This contained markers such as CD 19, CD 34, CD 10, CD58, CD 45, CD13, anti-TDT, CD33. Eight panels included were (1) CMPO-FITC/cCD79a-PE/cCd3ECD, (2) CD20-FITC/cCD10-PE/cCd-19ECD, (3) CD34-FITC/cCD117-PE/cCd45 ECD/CD2 PC 5, (4) CD15 FITC/CD33PE/CD45ECD, (5) CD14 FITC/CD13 PE/CD45ECD, (6) HLADR FITC/CD7 PE/CD45 ECD, (7) TdT FITC/CD45 ECD (IF CD34 NEG), and (8) CD58 FITC/CD 45 ECD (IF BOTH CD34 AND TdT NEG; were used to prepare the marker.
Results The study included 52 patients. In the 52 patients, 59.6% patients are alive with a p-value of 0.031. MRD was checked on every 15th and the 29th day and postconsolidation of the treatment where in day 15 (p = 0.023), it was 53.4% positive and 46.5% negative. On day 29 (p = 0.031), MRD was 22.5% positive and 77.5% negative, in post consolidation, it was positive in 20% and negative is 80%. MRD value below 0.01 is taken as negative and above is taken as positive. The overall survival (OS) is of 32.88 + 8.59 with a 6 to 36 months of duration. In In relapsed cases, no hemorrhagic relapse was found and two CNS relapse were found.
Conclusion It was a study of 52 patients of pBALL with a detection of MRD by FCM. MRD-negative patients had a good prognosis and comparatively lower rate of relapse than the one with positive MRD. Effort should be made to adhere to recommendation of MRD testing in clinical guidelines.
Epidemiology of Adolescent and Young Adult Cancers in a Tertiary Hospital in South India
Authors: Gupta Sahil , Palassery Rasmi , Devadas Santhosh K. , Maka Vinayak , Kilara Nalini 
Published: September 2021

Abstract
Introduction There has been an increase in the incidence of malignancies in young Indians, and there is no data reflecting the trend and profile of adolescent and young adult (AYA) cancers.
Objectives This study was aimed to ascertain the epidemiology of AYA cancers in a tertiary care center in south India and the trend of AYA cancers during the past 9 years.
Materials and Methods All patients aged 15 to 39 years with the diagnosis of cancer who were registered and received treatment with M.S. Ramaiah Hospital during a 9-year period from January 2011 to December 2019 were included. Basic demographic information on age, gender was available along with address and contact information. Using cancer site and morphology codes, the cancers were grouped by the ICD-O coding system of AYA cancers and their clinical information on disease and treatment status were collected retrospectively and analyzed.
Results Of the total 946 registered AYA cancer patients, majority of AYA cancer were in age group of 35 to 39 years (39%) and females (58%). When analyzing the data and dividing the AYA population into early (15–24 years) and late (25–39 years), we found that whereas the majority of the patients had hematolymphoid malignancies (48%) in the early group (15–24 years), the late group (25–39 years) had more carcinomas (68%). The percentage distribution of AYA cancers among the study population, lymphoma and leukemia contribute 11% and 15%, respectively, to the patient load and still the carcinomas formed the bulk (58%) of the population. It is interesting to know that breast, genitourinary, and gastrointestinal (GI) malignancies constituted 17.75%, 14.16%, and 14.69% individually.
Conclusion AYA oncology consists of a heterogeneous population and the profile differs by geography, sex, and other factors. There has been limited improvement in the past decade but there is a lot more to be done. To assess the problem, we have to identify and characterize the problem and look at the epidemiology of this population. This will require multicenter and international studies with focus on improving outcomes as in pediatric inspired ALL protocols. The trials should be started at local levels to ensure maximum participation. We need to generate data on epidemiology and channel our resources properly to save this precious but so called lost tribe of oncology.
Identification of impulsive adolescents with a functional near infrared spectroscopy (fNIRS) based decision support system
Authors: Erdoğan Sinem Burcu , Yükselen Gülnaz , Yegül Mustafa Mert , Usanmaz Ruhi , Kıran Engin , Derman Orhan , Akın Ata 
Published: September 2021

Abstract

Background. The gold standard for diagnosing impulsivity relies on clinical interviews, behavioral questionnaires and rating scales which are highly subjective. Objective. The aim of this study was to develop a functional near infrared spectroscopy (fNIRS) based classification approach for correct identification of impulsive adolescents. Taking into account the multifaceted nature of impulsivity, we propose that combining informative features from clinical, behavioral and neurophysiological domains might better elucidate the neurobiological distinction underlying symptoms of impulsivity. Approach. Hemodynamic and behavioral information was collected from 38 impulsive adolescents and from 33 non-impulsive adolescents during a Stroop task with concurrent fNIRS recordings. Connectivity-based features were computed from the hemodynamic signals and a neural efficiency metric was computed by fusing the behavioral and connectivity-based features. We tested the efficacy of two commonly used supervised machine-learning methods, namely the support vector machines (SVM) and artificial neural networks (ANN) in discriminating impulsive adolescents from their non-impulsive peers when trained with multi-domain features. Wrapper method was adapted to identify the informative biomarkers in each domain. Classification accuracies of each algorithm were computed after 10 runs of a 10-fold cross-validation procedure, conducted for 7 different combinations of the 3-domain feature set. Main results. Both SVM and ANN achieved diagnostic accuracies above 90% when trained with Wrapper-selected clinical, behavioral and fNIRS derived features. SVM performed significantly higher than ANN in terms of the accuracy metric (92.2% and 90.16%, respectively, p = 0.005). Significance. Preliminary findings show the feasibility and applicability of both machine-learning based methods for correct identification of impulsive adolescents when trained with multi-domain data involving clinical interviews, fNIRS based biomarkers and neuropsychiatric test measures. The proposed automated classification approach holds promise for assisting the clinical practice of diagnosing impulsivity and other psychiatric disorders. Our results also pave the path for a computer-aided diagnosis perspective for rating the severity of impulsivity.
Modern hydrological and morphological state of the Agrakhan Bay and its adverse changes
Authors: Magritsky D V , Samokhin M A , Sokolov D I , Erina O N , Goncharov A V , Tereshina M A , Surkov V V , Moreido V M , Arkhipkin V S , Semenova A A 
Published: September 2021

Abstract
The study was based, firstly, on the diverse data collected during field work in 2018 – 2020 in the eastern part of the Terek River delta and long-term hydrological monitoring data on the Roshydromet gauges. Secondly, on a profound comparative analysis of multi-temporal cartographic materials and multiple satellite images, laboratory analysis of water and sediment samples and other research groups’ field data. The performed analysis resulted in unprecedented complex and profound assessment of the contemporary hydrological, morphological and ecological state of the former Agrakhan Bay of the Caspian Sea. The drivers, dependencies and parameters of hydrological and morphological degradation were described; a multi-layer large-scale GIS was created to design multiple illustrations. The performed assessment allowed for development of measures for partial restoration of the hydrological and ecological potential of the former Agrakhan Bay.
Simulation of non-stationary two-phase mass transfer in a large reservoir
Authors: Rakhuba A V , Shmakova M V 
Published: September 2021

Abstract
The Kuibyshev Reservoir was formed on the Volga River and is the largest in Eurasia. The length of the reservoir along the Volga is 510 km with its maximum depth of 41 m and average depth of 8 m; the area of water mirror is 6,450 km2. Conditions of runoff formation in catchment area, as well as seasonal and daily regulation are the reasons for unsteady regime of the reservoir. Specificity of flow control in the Kuibyshev Reservoir predetermines water masses motion, flow speed pattern, as well as degree of water saturation with suspended sediments and, therefore, reservoir bed siltation intensity. The lowest flow velocity in the reservoir is observed in summer-autumn period of year; at this time, the reservoir bottom is reshaped least actively. During spring filling, flow velocity in the reservoir is at maximum, hence, favourable conditions to transfer small and large fractions of suspended sediments are created. Most of them enter the reservoir during its spring time filling, although sometimes, sediments maximum was observed earlier, before reaching the peak of flood wave in the reservoir. Flow pattern unsteadiness leads to increase or decrease in flow transfer capacity and, hence, changes in bottom levels. Complex configuration of banks, large depth gradients and basin morphology’s particulars pre-determine instability of sedimentation processes in water area. 3D hydrodynamic model of the reservoir (A. Rakhuba) forms the basis for calculating bottom level motions of the Kuibyshev reservoir. This model is supplemented with analytical formula for sediment consumption (M. Shmakova) and hydraulic ratios to calculate erosion and sediments accumulation (M. Shmakova). Four ice-free months runoff simulation of the Kuibyshev reservoir includes the following main water content phases: low water period and periods of snow flood and rain floods. The study of spatial and temporal patterns of bottom reshaping has shown that greatest intensity of such reshaping occurs during the period of large level gradients, i.e. high water. Flood swelling is featured by intensive bottom erosion. When flood recesses, transfer capacity decreases that leads to sedimentation. The greatest motions in bottom reshaping occurs in the places of channel contraction, which is explained by sharp changes in channel capacity.
Scenarios calculations of outburst flood and debris flows
Authors: Kurovskaia VA , Chernomorets SS , Vinogradova TA , Krylenko IN , Ghulomaidarov AG , Raimbekov YKh 
Published: September 2021

Abstract
The modelling results of outburst floods and debris flows, which can possibly occur in the Daraisit River Valley, are presented in this paper. The modelling was carried out according to 2 scenarios: the outburst of Lake Sist, the formation of a debris flow on a large tributary of the Daraisist River. The FLO-2D hydrodynamic model and the modernized transport-shear mudflow model developed by Yu.B. Vinogradov were applied in this study. The evaluation of the outburst flood discharge was carried out on the basis of a bathymetric survey. A digital elevation model (DEM) ALOS PALSAR with a resolution of 12.5 m was used as relief data for the valley, and survey data from an unmanned aerial vehicle (UAV) was applied for the debris flow fan. As a result, maps of the spatial distribution of velocities and depths for the rivers Daraisist and Pyanj were obtained. The most vulnerable areas within the Sist village were also identified.
River streamflow changes in the catchment of the Vilyuy reservoir, Eastern Siberia
Authors: Lebedeva L , Gustafsson D 
Published: September 2021

Abstract
The aim of the study is to assess river streamflow changes in the catchment area of the Vilyuy reservoir in the upstream area of the Vilyuy River, tributary of the Lena River. We analysed 2,556 time series with duration of 30, 35, 40 and 45 years sampled from the dataset of monthly discharges for eight hydrological gauges with data availability periods from 40 to 50 years. The result of a statistical trend test depends on the time series length and the coverage. The May and June river streamflow practically does not change. Most of the statistically significant positive trends were found in April, September and November. Among the eight gauges, the largest fractions of positive trends were found for the Akhtaranda River and the Vilyuy River, the northern tributaries of the Vilyuy Reservoir. Negative trends prevail on the Chona River that flows from the south and has discontinuous permafrost in the basin.
Assessment of irrecoverable retention of liquid atmospheric precipitation by meadow grass stands of the Middle Urals
Authors: Ye Klimenko D , Ostakhova A L 
Published: September 2021

Abstract
The process of retaining precipitation by grass vegetation is important in the processes of moisture circulation in forest landscapes. At the same time, there is an erroneous opinion that grasses are not able to retain a significant amount of rain moisture, which further forms the river flow. For this reason, the question remains poorly understood. In turn, grass stands are able to retain rainfall on their leaves in whole or in part. It depends on the duration and intensity of the rain. The leaves of grass stands have a specific morphology and are arranged more vertically than the leaves of woody plants; therefore, moisture on the leaves of grasses is held in film and drip forms (in woody plants-only in drip). When droplets roll down the stem, water is trapped in bowl-shaped recesses or funnels of grass leaves. The article discusses the relationship of precipitation and vegetation. The authors conducted field experiments on the retention of rainfall by grasses that grow in the landscapes of the Middle Urals. The experiments consisted of artificial sprinkling of grass samples and their subsequent weighing (weight experiments). In the course of the experiments, the connections were developed for the retention capacity of rain deposited on the leaves of species of grass vegetation with the leaf surface area of grass stands and their green mass. The magnitude of the loss of rainfall on grass stands is comparable with the magnitude of the rainfall of individual rains. According to the results of the experiment, it was found that under the forest canopy, the interception of precipitation is 0.1–0.2 mm, in the clearings – 1–2 mm, in the clearings – 2–4 mm. The results can be used to assess the actual rainfall to the surface of the soil and to calculate the change in the discharge of water from rain floods on rivers as a result of forest successions.
The influence of water masses to local climate of the Toktogul reservoir
Authors: Akmatov R T , Alamanov S K , Pochechun V A 
Published: September 2021

Abstract
The article is devoted to the analysis of the impact of the Toktogul Reservoir on the local climate in the context of global climate change. There is a global warming trend. In this regard, since the process of global warming is taking place on the territory of Kyrgyzstan, one of the most important scientific and practical issues is the assessment of the impact of the reservoirs built in Kyrgyzstan on the climate. The study found the Toktogul Reservoir has the effect of increasing air temperature. In the Ketmen-Tyube valley, the increase in air temperature depends on the volume of water in the Toktogul Reservoir. So, in the years of low water in the reservoir (1-6.5 billion m3), the average annual air temperature was 10.4°C, and in average water years (6.6-14 billion m3) 11.1 ° C and increased to 11.3°C in high-water years (14.1-19.5 billion m3).
Water management load on water resources of the Volga reservoirs
Authors: Shaporenko S I 
Published: September 2021

Abstract
Monitoring and assessment of anthropogenic load on water bodies is a permanent task of environmental protection. A complex parameter of water management load is suggested. It is calculated using the official water management statistics, and represented as a ratio of the utilization factor of river water runoff to the contribution of effluent treated to standard quality to the total amount that was required to be treated. Changes in the water runoff, water withdrawal and wastewater discharge in the sites of the Volga hydroelectric power stations by the periods from 1993 to 2018 were analysed. It is shown that the Ivankovo, Cheboksary and Gorky reservoirs experience maximum load on water resources. The first is due to the low river discharge and a high share of the withdrawal into the Moscow canal. Both others are due to poor wastewater treatment.
Temperature and humidity regime of the Volga basin in the period 1976-2019
Authors: Perevedentsev Y P , Shantalinsky K M , Sherstyukov B G , Mirsaeva N A , Aukhadeev T R , Parubova E M , Myagkov M A 
Published: September 2021

Abstract
The features of the distribution of air temperature and atmospheric precipitation on the territory of the Volga basin in the periods 1976-2019 and 2001-2019 are given. A positive trend in air temperature at the stations of the region in the period 1976-2019 both in the central months of the seasons, and throughout the year as a whole was revealed. A decrease in January air temperature was noted in the period 2001-2019. In general, an increase in atmospheric precipitation in the period under consideration is observed.
Changes in the annual and intra-annual river runoff of the Votkinsk reservoir’s catchment
Authors: Kalinin V G , Gyrdymov D A , Mekhanoshina E V 
Published: September 2021

Abstract
The assessment of the long-term variability of the rivers water content in the catchment area of the Votkinsk Reservoir for gauge stations (g/s) with the longest observation series (1939–2018) has been carried out. During the period under review, almost all g/s showed the presence of a statistically significant positive linear trend. The difference-integral curves revealed a violation of the stationarity of long-term observation series, and an analysis of the intra-annual distribution of monthly and seasonal runoff in% of the annual for two periods was carried out: 1956–1976 and 1977–2018. For the period 1977–2018 a decrease in the share of spring runoff (by an average of 7%), as well as an increase in the share of summer-autumn runoff and winter runoff by 18.4 and 24%, respectively, were found for almost all rivers in the study area.
Content of heavy metals in bed loads of gully systems within the limits of the Saratov city in summer season
Authors: Sheshnev A S , Majeed D S 
Published: September 2021

Abstract
The article presents the results of the analysis of the chemical composition of bed loads (layer of 0–1 cm) entering through streams in gullies from the limits of the Saratov city to the Volgograd Reservoir. The content of six heavy metals (Ni, Cu, Cd, Cr, Pb, Zn) having the property of accumulation and high toxicity were analysed. The most polluted sediments are found in gully systems, the drainage basins of which are located in industrial zones. The results demonstrate that in the absence of surface runoff treatment systems contaminated waters as well as soils enter water bodies from urbanized areas.
Migration and transformation routes of pharmaceutical substances in the aquatic environment
Authors: Kozlova M A , Shchegolkova N M 
Published: September 2021

Abstract
The paper considers the ways of migration and transformation of pharmaceutical substances in the aquatic environment. It is shown that the main source of pollution is insufficiently treated domestic wastewater. The occurrence of pharmaceutical substances is characterized by spatial and temporal variability. Some correlations in the distribution of certain groups of pharmaceuticals in water, sediments and suspensions are presented.
Contribution of microparticles to the transport of pollution by rivers and groundwaters in a large city
Authors: Yasinskii S V , Venitsianov E V , Kashutina E A , Sidorova M V , Ershova A A , Makeeva I N 
Published: September 2021

Abstract
Most components of the composition of natural waters exist in several phases – in the water mass, in suspensions, colloids, on Fe and Mn hydroxides, in detritus. They are often characterized by different toxicity. The smaller the particle of the suspension, the higher is its sorption capacity. Priority pollutants and their content in urban water bodies of Nizhny Novgorod in the summer-autumn low water period of 2020 were identified: organic substances, petroleum products, ammonium, surfactants, iron and manganese. More than half of their total transport is carried out by suspensions. In the estuaries of rivers with particles in the range of 0.22-2 microns, up to 70% of iron is carried by suspensions, up to 45% of manganese and about half of petroleum products and surfactants. Studied water objects (rivers, springs and water tunnels) are also polluted with synthetic microfibers of anthropogenic origin.