Miracle-dz/UniFAR-FTUs huggingface dataset:
Participation of MEM+ bacteria in the bacterioplankton community in Ustka harbor, the River Słupia estuary, Southern Baltic Sea

The number of bacteria was studied in the waters of the harbor canal in Ustka at the Baltic Sea. The studies were conducted with the use of the fluorescence microscope via live/dead method that differentiates the cells with the disintegrated membrane and live cells. The studies were conducted in a seasonal cycle at four research sites that differed in salinity and in the force of the influence of the marine environment. In all estuary zones the high percentage of dead bacteria (over 80%) was observed. The significant differences in number among particular sites were not observed. The relation between the number of live bacteria and the concentration of chlorides and organic matter was not demonstrated. It was showed that the number of bacteria falls within the greater seasonal fluctuation in the limnetic zone than in other estuary zones. Moreover, the very clear seasonal fluctuation of the studied parameters was observed. The maximum number of bacteria was stated in winter in the period of the lowest insolation.
Allele-level HLA matching reduces early rejection in lung transplant recipients

Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA Correspondence to: Raja Rajalingam, PhD. Professor of Clinical Surgery, Department of Surgery, Director, Immunogenetics and Transplantation Laboratory, University of California San Francisco, 3333 California Street, Suite 150, San Francisco, CA 94118, USA. Email: Rajalingam.Raja@ucsf.edu. Provenance and Peer Review: This is an invited article commissioned and reviewed by the Section Editor Jianfei Shen, MD (Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, China). Comment on: Zhang J, Liu D, Zhang C, et al. The value of high-resolution HLA in the perioperative period of non-sensitized lung transplant recipients. Ann Transl Med 2020;8:37.
Spatial Analysis to Evaluate Groundwater Vulnerability to Contamination of Unconfined Aquifer in Semarang Lowland Area Using DRASTIC Method

The increasing population up to 1.67% per year in the urban coastal city such as Semarang affects enormous stress on the natural resources – groundwater, in particular. To assess groundwater vulnerability to contamination the DRASTIC method was applied. DRASTIC was one method in compiling a zone of groundwater vulnerability to contamination. This method required seven parameters, namely D (water table depth), R (recharge zone), A (media aquifer), S (soil media), T (topography), I (vadose zone), and C (hydraulic conductivity). Processing of each parameter to calculate the Drastic Index (DI) was developed by using spatial analysis in ArcGIS. The results conduct there is three-level of groundwater vulnerability to contamination namely low, medium, and high. The low vulnerability has the number of DI of 61 to 100, while the DI of moderate is around 101-140. The high level is represented by 141-180 of DI. The low level is distributed in some areas in the south of Semarang, while the medium is dominated in the Ngaliyan area, Gajahmungkur, Semarang Selatan, also found in Tugu, Semarang Barat, Candisari, and some areas in the Semarang Tengah. Indeed, the high level is found in the plains areas in the northern, in the western, and eastern part of Semarang.
Circadian rhythms and biological clocks

Two new volumes of Methods in Enzymology continue the legacy of this premier serial with quality chapters authored by leaders in the field. Circadian Rhythms and Biological Clocks Part A and Part B is an exceptional resource for anybody interested in the general area of circadian rhythms. As key elements of timekeeping are conserved in organisms across the phylogenetic tree, and our understanding of circadian biology has benefited tremendously from work done in many species, the volume provides a wide range of assays for different biological systems. Protocols are provided to assess clock function, entrainment of the clock to stimuli such as light and food, and output rhythms of behavior and physiology. This volume also delves into the impact of circadian disruption on human health. Contributions are from leaders in the field who have made major discoveries using the methods presented here. * Continues the legacy of this premier serial with quality chapters authored by leaders in the field * Covers research methods in biomineralization science* Keeping with the interdisciplinary nature of the circadian rhythm field, the volume includes diverse approaches towards the study of rhythms, from assays of biochemical reactions in unicellular organisms to monitoring of behavior in humans.
Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases

1. The molecular biology data explosion 2. Introduction to genome browsing with the UCSC Genome Browser 3. Browsing with Ensembl, Map Viewer and other genome browsers 4. Interactive genome-database batch querying 5. Interactive batch post-processing with Galaxy 6. Introduction to programmed querying 7. Using the Ensembl API 8. Programmed querying with Ensembl, continued 9. Introduction to the UCSC API 10. More advanced application using the UCSC API 11. Customized genome databases 12. Genomes, browsers, databases - the future.
Ingestive and metabolic behavior of beef cattle fed diets with different levels of turnip forage (Rhaphanus sativus) cake in replacement to soybean meal

O objetivo deste trabalho foi avaliar a substituicao do farelo de soja pela torta de nabo forrageiro ( Rhaphanus sativus) no concentrado, sobre o consumo de materia seca, materia orgânica, proteina bruta, extrato etereo, fibra em detergente neutro e da fibra em detergente acido, pH e nitrogenio amoniacal (N-NH3) no liquido ruminal e ureia plasmatica em bovinos de corte. As racoes foram isoproteicas (6,5 %PB) e isoenergeticas (50,0 %NDT), sendo a silagem de cana-de-acucar in natura usada como volumoso (85,5% da MS). Foram utilizados cinco bovinos machos, castrados, ½ sangue Simental- Nelore, com peso medio de 610 kg e 36 meses de idade, todos fistulados no rumen. Os teores de substituicao do farelo de soja pela torta de nabo forrageiro foram: 0 (controle), 25, 50, 75 e 100%, com base na representacao proteica do farelo de soja na racao controle. Cada periodo experimental teve duracao de 19 dias. O experimento foi conduzido em um delineamento experimental em quadrado latino 5 x 5, sendo 5 animais e 5 periodos. O potencial de consumo de MS em %PV e em g/kg PV0,75 da torta de nabo forrageiro foi obtido com 27% de substituicao na base proteica em relacao ao farelo de soja, promovendo atraves desta, um consumo maximo de 0,217 kg/animal/dia, nao provocando alteracoes na dinâmica ruminal e no sangue.
Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.
The Stem Cells in Plants

In this opinion article, studies done on definition of stem cells in several plant species, genetic control and the areas in which these cells are applicated in past decades have been criticized. Key words: Stem cell, plant, pluripotency, shoot apical meristem, root apical meristem, cosmetics DOI: 10.7176/JSTR/6-02-01
Bird Nests and Construction Behavior

1. Animal builders and the importance of bird nests 2. The clutch-nest relationship 3. Standardising the nest description 4. Construction 5. The structure 6. The cost of nest building 7. The selection of a nest site 8. Bowers, building quality and mate assessment 9. The evolution of nest building Bibliography Index.
The effects of perch cooling on performance, carcass, and meat quality characteristics and behaviour of broilers reared at high temperatures with different litter thicknesses

The aim of the present study was to investigate the effects of cooled perch and litter thickness on performance, meat quality, carcass, and behaviour traits on broilers reared at high environmental temperatures. A total of 459 1 day-old male broiler chicks were randomly assigned to nine treatment groups based on the perch treatment (no perch, non-cooled perches, cooled perches) and litter thicknesses (1, 7 and 14 cm) with three replicates. Body weight was higher in broilers reared at cooled perch group at 6 wks (P<0.05). Body weight of chickens reared under the 1 cm thickness was found higher than the 7 and 14 cm of litter thickness chickens at 6 wks. Live and carcass weights, total breast and drum weights were higher in broilers reared at 1 cm litter thickness. The perch-contact incidence of chickens reared under the cooled perch was found higher than the non-cooled chickens for all hours at 6 wks. In conclusion, it is indicated that perch cooling and 1 cm of litter thickness have a beneficial effect on broiler performance exposed to high temperatures.
La búsqueda del sensor celular del oxígeno, un camino al Nobel

El premio Nobel de Medicina y Fisiologia ha sido otorgado este ano a los investi- gadores William Kaelin Jr., Sir Peter Ratcliffe y Gregg Semenza por descubrir los mecanismos moleculares mediante los cuales las celulas detectan los cambios en los niveles de oxigeno y se adaptan a ellos. Las celulas de un organismo requieren oxigeno para oxidar los nutrientes y generar energia. Sin embargo, los tejidos pueden verse temporalmente privados de oxigeno (hipoxia). Por ello, durante la evolucion las celulas han adquirido mecanismos que les permiten detectar cam- bios en los niveles de oxigeno y responder a ellos adaptando el metabolismo celular. Estos procesos adaptativos son fundamentales durante el desarrollo em- brionario y el mantenimiento de la homeostasis en adultos. Ademas, su desre- gulacion juega un papel fundamental en el desarrollo de enfermedades como la diabetes, el ictus o el cancer. En este articulo me centrare en el trabajo que realizo uno de los galardonados, William Kaelin, el cual fue mi jefe y mentor en mi etapa posdoctoral. El Dr. Kaelin descubrio los mecanismos subyacentes a la respuesta a hipoxia estudiando una enfermedad rara que se caracteriza por la aparicion de tumores altamente vascularizados, el sindrome de Von Hippel-Lindau. En la ac- tualidad, centra sus esfuerzos en el diseno de terapias dirigidas contra dianas multiples que, us das en combinacion, permitan en un futuro curar enferme- dades complejas como el cancer.
Original Article Gene Expression Profiles Associated with Advanced Pancreatic Cancer

Few studies have addressed the expression profiles associated with progression of pancreatic cancer to advanced disease. Towards this end, we performed expression profiling of a series of normal pancreas, pancreatitis and cancer tissues representing early stage resected pancreatic cancers (stages pT2/T3), late stage unresectable cancers (stage pT4) and matched metastases to a variety of organ sites. Microarray data was analyzed using linear modeling of microarray data (LIMMA), and differentially expressed genes were subjected to Gene Set Enrichment Analysis (GSEA). While robust differences were found in primary cancers as compared to normal pancreatic tissues, no differences were found between primary cancers and metastases, whether using matched or unmatched samples. When resected pancreatic cancers were specifically compared to advanced pancreatic cancers, significant differences in gene expression were found associated with growth at the primary site. These differentially expressed genes were most prominent in gene classes that related to MAPK and Wnt pathway, metabolism, immune regulation, cell-cell and cell-matrix interactions within the infiltrating carcinoma. One candidate upregulated gene (MXI1) was validated as having increased expression in advanced stage (T4) carcinomas by real-time PCR (p<0.05) and immunolabeling (p<0.003). We conclude that in addition to the robust changes in expression that accompany pancreatic carcinogenesis additional specific changes occur in association with growth at the primary site. By contrast, metastatic spread is not accompanied by reproducible changes in gene expression. These findings add to our understanding of pancreatic cancer and offer new topics for
The Cannabinoid 1 Receptor and Progenitor Cells in the Adult Central Nervous System

The aims of this chapter are to: (1) examine the key developments leading up to the discovery the cannabinoid 1 receptor (CB1R) and (2) assess the potential therapeutic benefits of cannabinoid drugs with respect to neurogenesis in the adult brain and spinal cord. As one of the most abundant G-protein coupled receptors found in the central nervous system, localization of CB1R and its role in the mature and in the developing brain will be discussed. Pharmacological studies with cannabinergic drugs, and studies utilizing knock-out mice of various endocannabinoid system components will be reviewed in the context of adult brain neurogenesis. The apparent conflicting data reveal the complexity of endocannabinoid signaling in this process. Though many studies have focused on CB1R and neurogenesis in the brain, none have evaluated the potential ability for CB1R to modulate the fate, and specifically neuronal differentiation, of adult spinal cord progenitors. The implications for CB1R modulation of adult neurogenesis are pivotal for understanding the behavioral and cognitive effects of chronic marijuana use, but also for assessing the potential consequences of pharmacotherapeutics with CB1R agonists or antagonists
The Solar System: Favored for Space Travel

Here, we compare Earth to the most common type of exoplanet, the super-Earth, with respect to interplanetary space travel. The typical super-Earth should have higher gravity and atmospheric pressure at its surface. These factors pose significant challenges to rocket launches and to reentering spacecraft. In addition, the Solar System is compared to exoplanetary systems with respect to interstellar travel. It is easier to launch an interstellar spacecraft from a planet in the circumstellar habitable zone of the Sun than from planets in the circumstellar habitable zones of less massive stars. In the larger context of the Milky Way galaxy, our Solar System is in the best location to initiate interstellar missions. In summary, we here confirm and expand upon recent studies that argue that the Earth and the Solar System are rare in the degree to which they facilitate space exploration.
Insights into the dynamics of the deep hypolimnion of Lake Geneva as revealed by long‐term temperature, oxygen, and current measurements

In order to identify or shed light on dominant long‐term processes of the deep hypolimnion of Lake Geneva (309 m depth), time series of temperature and horizontal currents and profiles of temperature and oxygen, taken for over a decade in the deepest part of the lake, were analyzed. The focus was on the summer stratification period (May to October). During that period, temperatures near the bottom always increased quasi‐linearly with the same gradient and small amplitude variability. Vertical mean temperature gradients in the lowest 60 m of the water column remained nearly constant over the years and were comparable to those of the deep ocean. Mean current velocity at the deepest point was 3.0 ± 0.5 cm s−1 and ever‐present inertial motions clearly dominated currents. Oxygen decreased quasi‐linearly and eutrophication appeared not to affect this rate of decrease. It is suggested that as in the deep ocean, breaking internal waves and friction from decaying inertial motion occurring in the deep hypolimnion strongly contribute to turbulent mixing in that layer. The climate change‐induced long‐term warming trend seen in the upper layers of the lake was not detected in the deep hypolimnion. Instead, year‐to‐year climate change‐induced variability strongly affected the deep hypolimnion. During cooling in cold winters, lateral advection contributed more to temperature decrease and oxygen renewal in the deep hypolimnion than vertical convection. The present analysis has shown that the dynamics of this layer are highly three‐dimensional and that the processes occurring therein cannot be correctly described by traditional one‐dimensional concepts.
Cytogenetic Studies on Rat Leukemia Induced by Pulse Doses of 7,12-Dimethylbenz(α)anthracene

Summary Cytogenetic studies were carried out on bone marrow and spleen cells of 40 rats of Long-Evans strain with primary leukemia induced by pulse doses of 7,12-dimethylbenz(α)anthracene. Chromosomal abnormalities were detected in 26 cases, of which 21 were characterized by abnormal constitution of two specific chromosomes, C-1 (longest telocentric chromosome), and A-6 (6th group of metacentrics). Most of the leukemias represented the hepatic type. Sixteen rats had modal or nonmodal cells with trisomic C-1 chromosome, 5 among them containing stem-line cells with both C-1 and A-6 trisomy. Unassociated A-6 trisomy was found in modal cells of 4 other leukemias, one of them chloroleukemia, and in the stemline of one of the trisomic C-1 positive leukemia. Modal hypodiploid cells of 41 chromosomes with A-6 monosomy was also detected in one case. These consistent chromosomal abnormalities appear to be the first so far reported for an experimental leukemia. The presence of a marker chromosome, metacentric or submetacentric, was recognized in cells of 4 other leukemias. The remaining one had tetraploid cells. No chromosomal anomaly could be detected in 12 other hepatic type leukemias, one lymphoblastic and another thymic. The possible interpretation for the presence of consistent chromosomal abnormalities in the given type of leukemia is discussed.
Contingency Based Tourism Village Managerial: Proposed Development of Eco-Village Tourism in Bantul Regency.

This research aims to review the theoretical study of contingency theory and the concept of entrepreneurship in the context of submitting research prepositions about antecedent factors and the consequences of management patterns of eco-village tourism. Observations are planned to be carried out using a sample of 11 tourist villages in Bantul Regency and data collection is carried out by in-depth interview techniques with 25 research participants including community leaders, business people and government officials who manage Small and Medium Enterprises (SME). More detailed this paper explores the external and internal environmental factors that have a significant influence on the managerial pattern of eco-friendly tourism villages. Managerial pattern dimensions include the intensity of innovation, pro- active behavior and business agility are also predicted to determine the success of the management of environmentally friendly tourism villages.
Simulation and Testing of Cylindrical Magnetic Turbine Design at the Center for Innovation and Certification (CIC)

Cylindrical magnetic turbine design with a stator diameter of 13.7 cm and a rotor diameter of 10.7 cm has a distance between the magnets on the rotor and stator is 1.7 cm with zigzag configuration. Turbine simulation with FEMM 4.2 results the largest density flux can be between 5.091e-001 5.690e-001 Tesla, with the value of the thrust on the x-axis having a maximum value of 0.0976232 N, while the y-axis has a maximum value of 0.067278 N. Torque the maximum obtained in a magnetic turbine is 0.5011 Newton meter. Direct testing results magnetic turbines have a maximum turbine rotation speed 12.22 12.92 rpm with a rotation time 14 16 seconds.
Drinking Water Temperature around the Globe: Understanding, Policies, Challenges and Opportunities

Water temperature is often monitored at water sources and treatment works; however, there is limited monitoring of the water temperature in the drinking water distribution system (DWDS), despite a known impact on physical, chemical and microbial reactions which impact water quality. A key parameter influencing drinking water temperature is soil temperature, which is influenced by the urban heat island effects. This paper provides critique and comprehensive summary of the current knowledge, policies and challenges regarding drinking water temperature research and presents the findings from a survey of international stakeholders. Knowledge gaps as well as challenges and opportunities for monitoring and research are identified. The conclusion of the study is that temperature in the DWDS is an emerging concern in various countries regardless of the water source and treatment, climate conditions, or network characteristics such as topology, pipe material or diameter. More research is needed, especially to determine (i) the effect of higher temperatures, (ii) a legislative limit on temperature and (iii) measures to comply with this limit.
Structural and Functional Characterization of the MBD2-NuRD Co-Repressor Complex

xv CHAPTER 1: Introduction . 1 I. Hemoglobin and the hemoglobin switch: . 1 A. Hemoglobin . 1 B. The β-globin gene locus and the hemoglobin switch: . 2 II. Erythropoiesis: . 5 III. β-hemoglobinopathies: . 7 A. Sickle Cell Disease (SCD) . 8 B. β-thalassemias . 11 C. Management of β-hemoglobinopathies: . 15 i. Therapeutic options for β-hemoglobinopathies: . 15 ii. Fetal Hemoglobin Stimulants: . 16 iii. Futuristic therapeutic options: . 19 IV. Human β-globin gene regulation . 21