jimnoneill/paper-to-field-training huggingface dataset:
Molecular dissection of a genome defense pathway in Neurospora crassa

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Meiotic silencing by unpaired DNA (MSUD) is an RNA interference (RNAi) pathway in Neurospora crassa that detects genes without a homologous partner and silences them for the duration of sexual development. In this study, we have further elucidated the function of known MSUD proteins, identified novel proteins that are required for MSUD, and demonstrated the conservation of RNAi-related processes at the nuclear periphery. We began by showing SAD-2 is crucial for the localization of other MSUD proteins in the perinuclear region. These data suggest that SAD-2 works as a scaffold protein and that proper function of MSUD, like other germline RNAi-like systems, is reliant on the presence of silencing proteins in the perinuclear region. An MSUD suppression assay identified two novel MSUD proteins, SAD-Y and SAD-B'. Even though SAD-Y and its homologs contain a conserved putative RNA- binding motif, they have yet to be assigned to a biochemical pathway. Our work here has linked silencing to SAD-Y-like proteins. SAD-Y has been shown to interact with other MSUD factors in both the nucleus and at the nuclear periphery. SAD-B's homolog has been found in the nuage, an epicenter for RNA-binding proteins involved in post-transcriptional regulation for Drosophila germline cells. SAD-B interacts with core MSUD proteins and has an especially intimate association with SMS-2, which requires it for localization. Furthermore, bimolecular fluorescence complementation (BiFC) revealed that SAD-B' interacts with a Golgi retrograde transport protein and an autophagy marker protein, suggesting the importance of the endomembrane system in this RNAi process.

Topic: Insect Resistance and Genetics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Effects of 1‐methylcyclopropene combined with modified atmosphere on postharvest quality and cell wall metabolism of <i>Zizania latifolia</i>

Abstract During postharvest storage, the metabolism of cell wall components greatly affects the quality of fruits and vegetables. Utilizing 1‐methylcyclopropene (1‐MCP) as an ethylene receptor inhibitor and modified atmosphere (MA) separately or in combination (1‐MCP+MA) were investigated for their impact on Zizania latifolia quality during postharvest storage. The treatments effectively controlled firmness increase, color degradation, and reductions in soluble protein, reducing sugar, total phenol, and ascorbic acid content, with the combined 1‐MCP+MA showing the most significant effect. These treatments also moderately changed soluble pectin, protopectin, cellulose, and hemicellulose content, preserving the activities of essential enzymes and the expression of enzyme genes. The combined treatment particularly demonstrated superior preservation capabilities, holding promise for reducing postharvest losses and maintain the storage quality of edible produce, offering insights for efficient postharvest storage and freshness maintenance of fruits and vegetables.

Topic: Plant Physiology and Cultivation Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Geometric morphometric analyses define riverine and lacustrine species flocks of Himalayan snowtrout (Cyprinidae: Schizothorax) in Nepal

Freshwater fishes in the river and lake systems in the Himalayas and Tibetan Plateau are morphologically diverged but the evolutionary relationship of putative subspecies separated in these freshwater systems has not been explored. Snowtrout ( Schizothorax spp.) are minnows (Cyprinidae) broadly distributed in Asia. Body shapes of 3 Lake Rara (northwest Nepal) endemics ( S. macrophthalmus , S. nepalensis , S. raraensis ) and 2 widely distributed riverine species ( S. progastus , S. richardsonii ) across 3 drainages in Nepal (i.e. Karnali, Gandaki, and Koshi Rivers) were studied using geometric morphometry. Data were derived from museum voucher specimens/tissues collected in 1984-1986 and 1996 (Lake Rara). Cartesian coordinates of 18 anatomical points (Type I landmarks) from 528 individuals were digitized; shape variation was then quantified with principal component analysis and visualized with thin-plate splines derived from a Procrustes analysis. Models of shape variation (i.e. taxonomy versus geography) were tested with a multivariate analysis of variance and a morphological distance matrix. Phylogeographic relationships were examined with a haplotype network (N = 115) derived from 1140 base pairs of the mitochondrial DNA cytochrome b gene, and selected GenBank sequences (N = 5). Koshi River snowtrout diverged morphologically from conspecifics, consistent with the phylogeographic data. In contrast, Gandaki and Karnali River snowtrout grouped by morphotype (up- versus downstream) irrespective of geographic origin, yet clustered separately within the haplotype network. Lake Rara snowtrout were morphologically but not genetically distinct, due to incomplete lineage sorting. Morphological and genetic variability in Schizothorax from Nepal represent a mosaic driven by isolation (= vicariance) and specialization (= adaptation), with taxonomy insufficiently reflecting diversity. Additional data are required to appropriately derive management and effective conservation plans.

Topic: Fish Biology and Ecology Studies
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Long-term endoscopic management for primary recurrent pyogenic cholangitis

Abstract Background: Primary recurrent pyogenic cholangitis (RPC) is characterized by relentless suppurative cholangitis in those with a suspected parasitic injury of the biliary tree. Prior work has demonstrated that the infections recur following “definitive” biliary surgery and long-term percutaneous biliary catheters are poorly tolerated. The aim of this study was to assess whether scheduled surveillance endoscopic retrograde cholangiopancreatography (ERCP) prevents cholangitis in those with RPC. Materials and Methods: Following initial biliary decompression and stone clearance, patients with RPC were offered serial ERCP every 3-6 months to remove accumulating stony debris and to dilate incipient strictures. Review of a large series managed using this approach at the University of California, San Francisco Medical Center was performed. The principle outcome was the development of acute cholangitis requiring hospitalization and whether the episode occurred, while the RPC patient was in compliance with endoscopic surveillance recommendations. Results: Over a period of 10 years, 66 patients with primary RPC were managed for RPC at the University of California, San Francisco. The patients were comprised primarily of first-generation immigrants from Asia though one-quarter had migrated from Latin America and Russia. Episodes of cholangitis were significantly less likely to occur in those undergoing surveillance biliary endoscopy than in those who were not (odds ratio 5.3; P = 0.005). The mean follow-up was 36.1 months. Conclusions: Serial endoscopic treatment of RPC may be used to systematically clear biliary debris and decreases the risk of cholangitis requiring hospitalization. It represents a reasonable initial management strategy for these patients. Surgery and percutaneous management may also be required, but are best performed as part of a multidisciplinary approach.

Topic: Gallbladder and Bile Duct Disorders
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Great Plains Coal Gasification Plant Water Balance Start-Up and Operation

Abstract The Great Plains Coal Gasification Plant near Beulah, in Western North Dakota is now in operation producing high quality substitute natural gas (SNG) from lignite coal. Plant start-up began in August 1983 with commissioning of the water treatment plant. On April 24, 1984, the first gasifier was operated on steam and oxygen. The first pipeline quality gas was produced July 28, 1984. The entire plant was onstream by the end of November 1984 meeting the planned 15-month start-up schedule. The plant produced SNG at 68 percent of the 137.5 million standard cubic feet per day (3.894 million standard cubic meters per day) design capacity during December 1984 and January 1985. Debottlenecking projects are underway to allow design capacity operation in 1985. The Great Plains plant has a highly integrated water system. Lake water is used for make-up at rates of 3,700 to 4,900 GPM (14,000 to 18,500 LPM) winter to summer. The plant does not surface discharge treated process wastewater. Most of the process wastewater is used as cooling tower make-up. A large quantity of water is also consumed in the gasification process. The cooling tower is operated as an aerobic biological treatment system. Most of the water entering the plant leaves as evaporation from the cooling tower. A large quantity of water is also consumed in the gasification process. The remainder, inorganic wastewater, is injected in deepwells. The plant water balance is complex with many interrelationships between the water treatment, steam, cooling water, wastewater treatment, and process units. The water balance was a significant constraint during start-up and continues to be a major factor in plant operation.

Topic: Landfill Environmental Impact Studies
Subfield: Industrial and Manufacturing Engineering
Field: Environmental Science
Domain: Physical Sciences
Design on a phase method PSD micro-displacement measurement system based on LabVIEW

PSD detection technique based on phase method has advantages of simple processing circuit,high detecting precision,strong anti-interference ability and good environmental adaptability,compared with amplitude method.A micro-displacement measurement system based on LabVIEW and 2D duo-lateral PSD is designed.Experimental results reveal that the phase difference of the PSD output signal and the light spot position have good linear relation,and the nonlinear error is less than 0.1 %.

Topic: Advanced Optical Sensing Technologies
Subfield: Instrumentation
Field: Physics and Astronomy
Domain: Physical Sciences
Mechanisms of Anthraquinone Inhibition of Sulfate-Reducing Bacteria

Abstract This paper presents evidence that anthraquinone derivatives can be generally useful for preventing sulfide production from sulfate-reducing bacteria (SRB). We believe there is unique value for these compounds in oilfield and industrial applications where cost-effectiveness and human and environmental safety are of paramount importance. It has been previously shown that anthraquinones inhibit sulfate respiration, but not aerobic respirations. This aspect permits safe use in wastewater treatment applications where aerobic microbial activity is required. We propose that this specificity is due to the ability of anthraquinones to randomly equilibrate electron flow in the membranes of bacteria of the genus Desulfovibrio. A consequence of this equilibration is that ATP synthesis is uncoupled from respiration. Since sulfate activation has a unique requirement for ATP, sulfate reduction halts with the depletion of ATP level. In this report a positive correlation is shown between inhibition of sulfate respiration by anthraquinones and their reactivity with cytochrome c3, which is a protein considered to be diagnostic of SRB. A model is discussed for involving anthraquinone mediated electron transfer around energy-conserving sites, resulting in a loss of ATP synthesis. This scenario is consistent with the specific inhibition of sulfate respiration in contrast to other respiration processes which do not require ATP. Inhibition of SRB within a biofilm is dependent upon the species of the anthraquinone and the system hydraulics surrounding the biofilm. Bioavailability of anthraquinone is discussed in terms of soluble and insoluble species of anthraquinone and their mobility within the biofilm. Due to low toxicity, we believe that certain anthraquinones provide an environmentally acceptable alternative to highly toxic biocides for the control of SRB in oilfield water systems.

Topic: Enhanced Oil Recovery Techniques
Subfield: Ocean Engineering
Field: Engineering
Domain: Physical Sciences
Enhancement of quantum efficiency in thin photodiodes through absorptive resonance

The spectral response of resonantly enhanced photodiodes is analyzed theoretically and verified experimentally. Comprehensive design guidelines and formulas are given for device structures containing a metal reflector, a contact layer, and optional grading layer, an absorbing layer, and a quarter-wave stack (QWS). The analysis shows, for instance, that the quantum efficiency of a Schottky photodiode with a 162-nm GaInAs absorbing layer can be enhanced 3.7-fold by using a 41-layer AlInAs/AlGaInAs QWS. The number of layers required could be much lower for other material systems and/or if the substrate is removed. Experimentally, 50% enhancement is demonstrated for a 475-nm-thick absorbing layer at 1.52 mu m by using a 16-layer QWS. The resonance width is approximately 4.4%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Topic: Semiconductor Quantum Structures and Devices
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Simulation of electron trajectories in nuclear emulsion and its application

Atsushi Iyono∗a, Saya Yamamotob, Hiroki Matsumotoc, Kazuhide Okeic and Takao Nakatsukad, aDept. of Fundamental Science, Faculty of Science, Okayama university of Science 1-1 Ridai-cho, Kita-ku, Okayama-city, Okayama 700-0005, Japan bGraduate School of Science, Okayama University of Science 1-1 Ridai-cho, Kita-ku, Okayama-city, Okayama 700-0005, Japan cKawasaki Medical School 577 Matsushima, Kurashiki-city, Okayama 701-0192, Japan dOkayama Shoka University 2-10-1Tsushima Kyomachi, Kita-ku, Okayama-city ,Okayama 700-8601, Japan E-mail: iyono@das.ous.ac.jp,s15sm08@ous.jp,h.matsumoto@med.kawasaki-m.ac.jp, okei@med.kawasaki-m.ac.jp,nakatuka@olive.plala.or.jp

Topic: Radioactive Decay and Measurement Techniques
Subfield: Radiation
Field: Physics and Astronomy
Domain: Physical Sciences
Shady Grove Site (22QU525) Quitman County, Mississippi: Analysis of Demographics and Mortuary Practices

The Mississippian Period (A.D. 1000-1500) is distinguished by reliance on stable agriculture, sedentary ranked populations, and production of prestige goods. Sociopolitical structure was based on kinship, wealth, and power, and can be revealed through the local mortuary programs. This thesis explores the mortuary practices observed at an ossuary at Shady Grove (22QU525), a small mounded center in Quitman County dating to the Early Mississippian Period, based on demographics, burial mode, cemetery location, and associated grave goods. The Burial 43 ossuary, excavated in 2010 contained stacked bundle burials of at least 78 individuals. All age groups and both sexes were present. There were 22 artifacts recovered, including 12 shell tempered vessels and a copper ornament. There were both collective offerings to the entire group and several artifacts interred with two individuals, which may indicate they were persons of higher status. It is unclear if the ossuary contains a single kin group or a sample of the entire population, which would indicate that everyone was allotted equal access to both locally produced and trade items. The observed difference in the burial method of stacked burials and its location under Mound B shows the variability of mortuary practices during this time period in the region. The information gained from this study will help in the understanding of the sociopolitical organization of smaller chiefdoms in the Mississippi Delta and Lower Mississippi Valley.

Topic: Archaeology and Natural History
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences
Electromagnetic Diffraction of a very Obliquely Incident Plane Wave Field by a Wedge with Anisotropic Impedance Faces

An asymptotic solution in the format of the uniform geometrical theory of diffraction (UTD) for the field diffracted by an anisotropic impedance wedge has been presented, when the wedge is illuminated by an arbitrarily polarized plane wave impinging at very skew incidence on its edge. The surface impedance tensor principal anisotropy axes are along directions parallel and perpendicular to the edge. The solution is derived by resorting to the perturbation technique with respect to the oblique incident angle based on an exactly solved special case: grazing to the edge incidence. The numerical examples provide a uniform and continuous behaviour of the field with respect to the observation angle.

Topic: Electromagnetic Scattering and Analysis
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Role of vesicles during adenovirus 2 internalization into HeLa cells

In this investigation, the early period of adenovirus type 2 (Ad2)-HeLa cell interaction was analyzed by electron microscopy and biochemical techniques. Events observed in this period ranged from the disappearance of virions from the cell surface to their subsequent association with the cell nucleus. Destabilization of the virions attached to the intact cell was necessary for virions to escape from intracellular vesicles. Strong temperature dependence and rapid escape from a vesicular compartment were shown in temporal kinetic experiments. These vesicles appeared to be acidic, since lysosomotropic agents partly inhibited the release of virions from vesicles. Studies of Ad2 binding to cells in buffers of different pH values suggested that adenovirus binds to cells by two different mechanisms. At low pH the binding was most probably mediated by the penton base and at neutral pH by the fiber protein. The number of receptor sites per cell was 25,000 and 6,000 at low and neutral pH, respectively. This study suggests that the low-pH affinity between the penton base and a vesicular membrane is important inside acid vesicles when Ad2 quickly enters the cytoplasm. However, a significant fraction of the virions was possibly internalized by a pathway not requiring a passage through such vesicles.

Topic: Virus-based gene therapy research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Association of Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism in breast cancer patients of Bihar: Case-control study

Breast cancer (BC) is the most frequent cancer in women globally and the main cause of cancer-related mortality. MTHFR C677T is a functional polymorphism in the genes encoding a one-carbon metabolism enzyme that affect folate metabolism and may be associated with breast cancer susceptibility. We have conducted a case-control study taking 100 cases of diagnosed breast cancer and 100 healthy control. PCR-RFLP technique was used to detect the genotype of C677T polymorphism in the study population. About 35% of cases had normal genotype(C677C), 49% had the genotype C677T &amp; rest 16% had the genotype T677T for MTHFR. Among control the frequency of C677C genotype was 55% C677T was 40% &amp; T677T was 5%. C677T &amp; T677T MTHFR genotype were more common in case as compared to control [χ2 (2, N = 200) = 11.12, p = 0.004]. T allele frequency was significantly higher in case (40%) as compared to control (5%) [χ2 (1, N = 400) = 10.91, p = 0.001]. Cases with MTHFR 677TT genotype had a significantly higher risk of BC than 677CC individual [OR=1.64 (1.03 to 2.10)] and increasing T-allele was significant in BC [OR=1.07 (0.71 to 1.33)] (P for trend = 0.04). C677T of MTHFR gene has a strong correlation with breast cancer in the studied population and can be used as a prognostic marker for the development of breast cancer.

Topic: Folate and B Vitamins Research
Subfield: Rheumatology
Field: Medicine
Domain: Health Sciences
Spectroscopic Study of Ni(II)-4, 4’, 4’’, 4’ ’’ – Tetrasulfophthalocyanine In Aqueous Solution

It was determined spectrally that a monomer-dimer equilibrium exists in aqueous solutions of Ni-TSPC4- over a concentration range of 5 x 10-8 – 10-4 M. Equilibrium measurements were made under natural ionic strength conditions at 29°, 39° and 49°C. The values obtained for the equilibrium constants at 29°, 39° and 49°C were 2.4 x 108, 6.6 x 107 and 2.9 x 107 M-1, respectively. These results indicated that the equilibrium strongly favors dimer formation. This study also showed that nickel is second to copper in enhancing the dimerization of metallotetrasulfophthalocyanine complexes. However, metals in general inhibit dimer formation relative to the free ligand. The dimerization reaction of Ni-TSPC4- is exothermic with thermodynamic parameters of ΔG° = -11.6 kcal/mole, ΔH = -20.9 kcal/mole, and ΔS = -31 e.u. The dimerization process is thus favored from an energetic point of view despite the unfacorable entropy change.\nSpectral measurements made on Ni-TSPC4- in aqueous pyridine solutions in the concentration range of .05 - 6.0% pyridine (by volume) indicated a dipyridinated dimer complex of Ni-TSPC4- was formed. Using a modified version of the Benesi-Hildebrand equation, the following equilibrium was proposed : D + 2Py = D(Py)2. The overall equilibrium constants for this system at 15°, 21°, 30° and 40°C were 1.7, 1.9, 2.8, 3.6 and 4.4 M-2, respectively. The equilibrium reaction is endothermic with thermodynamic parameters of: ΔG=6.2 kcal/mole, ΔH =6.9 kcal/mole, and ΔS=25 e.u. Thus, the equilibrium reaction was favored thermodynamically due to the favorable entropy change associated with the process.\nLigand studies indicated that only pyridine and polupyridine ligands bind to Ni-TSPC4- and cause a spectral change. This study also showed that Ni-TSPC4- cannot be used as an oxygen carrier in biological systems.

Topic: Porphyrin and Phthalocyanine Chemistry
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
The Reduction of Neptunium(VI) by Basalt and Olivine

The interaction of Np(VI) in 0.1 M NaHCO3 solution, distilled water, or artificial seawater with basalt or olivine results in the production of Np(V) and Np(IV). The rate of increase in Np(V) was determined over periods of 120 (olivine substrates) and 140 days (basalt substrates). The Np(V) that does not remain in solution is preferentially adsorbed on the surface of the minerals as compared to the surface of the containers. The mechanism for the production of Np(IV) and Np(V) postulates adsorption and desorption steps for the aquo Np(VI) and Np(V) ions on to the silicate surface. The electron transfer reaction takes place when the Np(VI) or Np(V) is adsorbed on this surface at an Fe(II) site. Reduced neptunium ions are then adsorbed from the solid.

Topic: Radioactive element chemistry and processing
Subfield: Inorganic Chemistry
Field: Chemistry
Domain: Physical Sciences