Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Autoimmunity-Related Gene CLEC16A in the B Cell Receptor–Mediated HLA Class II Pathway

Key Points CLEC16A correlates to surface CLIP expression in human B-LCLs and primary B cells. CLEC16A knockdown impairs BCR-mediated uptake of Ag into MIICs. CLIP is abundant and not coregulated with CLEC16A in blood B cells of MS patients. Visual Abstract C-type lectin CLEC16A is located next to CIITA, the master transcription factor of HLA class II (HLA-II), at a susceptibility locus for several autoimmune diseases, including multiple sclerosis (MS). We previously found that CLEC16A promotes the biogenesis of HLA-II peptide-loading compartments (MIICs) in myeloid cells. Given the emerging role of B cells as APCs in these diseases, in this study, we addressed whether and how CLEC16A is involved in the BCR-dependent HLA-II pathway. CLEC16A was coexpressed with surface class II–associated invariant chain peptides (CLIP) in human EBV-positive and not EBV-negative B cell lines. Stable knockdown of CLEC16A in EBV-positive Raji B cells resulted in an upregulation of surface HLA-DR and CD74 (invariant chain), whereas CLIP was slightly but significantly reduced. In addition, IgM-mediated Salmonella uptake was decreased, and MIICs were less clustered in CLEC16A-silenced Raji cells, implying that CLEC16A controls both HLA-DR/CD74 and BCR/Ag processing in MIICs. In primary B cells, CLEC16A was only induced under CLIP-stimulating conditions in vitro and was predominantly expressed in CLIPhigh naive populations. Finally, CLIP-loaded HLA-DR molecules were abnormally enriched, and coregulation with CLEC16A was abolished in blood B cells of patients who rapidly develop MS. These findings demonstrate that CLEC16A participates in the BCR-dependent HLA-II pathway in human B cells and that this regulation is impaired during MS disease onset. The abundance of CLIP already on naive B cells of MS patients may point to a chronically induced stage and a new mechanism underlying B cell–mediated autoimmune diseases such as MS.
Continuity or replacement: Controversies in homo sapiens evolution. Edited by Gunter Bräuer and Fred H. Smith. Rotterdam, Netherlands and Brookfield, VT: A. A. Balkema. 1992. xi + 315 pp. ISBN 90‐6191‐149‐4. $85.00 (cloth)

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Direct-Observation Cohort Study of Shared Decision Making in a Primary Care Clinic

Background. Observational studies suggest that shared medical decision making (SMDM) is suboptimal. Our objective was to assess patient preferences, ratings, and objective measurements of decision making and their impact on patient outcomes. Methods. Hypertensive adults presenting for routine care with their primary care physician completed previsit surveys assessing SMDM preferences. Postvisit surveys assessed the degree of SMDM during the encounter, patient satisfaction, and trust. Encounters were audiotaped and transcripts were coded for type of decisions made as well as SMDM quality using OPTION-5. Adherence and blood pressure were measured at baseline and at 4 weeks. Results. Among 105 encounters, there were 7.4 decisions per visit; most were basic, such as refills and routine testing. Objective measures of decision making indicated that the degree of SMDM was lower than reported by patients or physicians, although physician ratings were more accurate. Previsit, 54% of patients expressed a desire for equally shared medical decision making, 24% preferred physician dominated decision making, and 18% preferred that they make the decisions. Postvisit, patients reported experiencing SMDM in 57% of encounters, with high concordance between desired and perceived decision making. Discordance between the patient’s desired and experienced SMDM reduced trust and satisfaction. The quality of shared decisions had no impact on adherence or blood pressure at 4 weeks. Limitations. Single site, small sample. Conclusions. Decisions are common during internal medicine primary care visits, and most are basic. Most patients preferred SMDM, and their perceptions of the visit decision-making style were concordant with their preferences although higher than objective measures suggested. Physician ratings of the quality of SMDM were more accurate than patient ratings. Discordance between patients’ expected and experienced SMDM lowered satisfaction and trust.
Element stoichiometries of individual plankton cells collected during the Southern Ocean Iron Experiment (SOFeX)

During the Southern Ocean Iron Experiment (SOFeX), we analyzed Si, P, S, Mn, Ni, and Zn in individual diatoms, autotrophic flagellates, and heterotrophic flagellates with synchrotron‐based X‐ray fluorescence (SXRF) and calculated cellular C from measurements of cell size. Element stoichiometries for the different types of protists (normalized to either C, S, or P) were generally in good agreement with prior bulk analyses of natural assemblages but also revealed previously undocumented differences in elemental composition among cell types. Flagellated cells contained 39% more P than diatoms, which in turn contained 79% more Mn, 3‐fold more Ni, and 2.6‐fold more Zn than flagellates. Heterotroph cells contained approximately 40% more P and twice as much Zn as autotrophs. Manganese and Ni stoichiometries were negatively related to cell volume, while larger cells contained more Zn per mole C. Iron fertilization resulted in an approximate doubling of Mn, Ni, and Zn quotas and smaller increases in cellular P, but the timing of the stoichiometric changes varied between the two patches. Silicon contents of diatoms dropped approximately 40% after the first Fe addition but returned to prefertilization levels as cellular P doubled following the second addition, resulting in 40% lower Si : P ratios in the fertilized waters. The mean elemental stoichiometries calculated for all cells analyzed were comparable with previously published extended Redfield ratios for mixed plankton assemblages, but the observed differences between diatoms and flagellates and between autotrophs and heterotrophs indicate that valuable information is lost when all types of co‐occurring plankton are grouped together for analysis.
Sources of plant‐derived carbon and stability of organic matter in soil: implications for global change

Alterations in forest productivity and changes in the relative proportion of above‐ and belowground biomass may have nonlinear effects on soil organic matter (SOM) storage. To study the influence of plant litter inputs on SOM accumulation, the Detritus Input Removal and Transfer (DIRT) Experiment continuously alters above‐ and belowground plant inputs to soil by a combination of trenching, screening, and litter addition. Here, we used biogeochemical indicators [i.e., cupric oxide extractable lignin‐derived phenols and suberin/cutin‐derived substituted fatty acids (SFA)] to identify the dominant sources of plant biopolymers in SOM and various measures [i.e., soil density fractionation, laboratory incubation, and radiocarbon‐based mean residence time (MRT)] to assess the stability of SOM in two contrasting forests within the DIRT Experiment: an aggrading deciduous forest and an old‐growth coniferous forest. In the deciduous forest, removal of both above‐ and belowground inputs increased the total amount of SFA over threefold compared with the control, and shifted the SFA signature towards a root‐dominated source. Concurrently, light fraction MRT increased by 101 years and C mineralization during incubation decreased compared with the control. Together, these data suggest that root‐derived aliphatic compounds are a source of SOM with greater relative stability than leaf inputs at this site. In the coniferous forest, roots were an important source of soil lignin‐derived phenols but needle‐derived, rather than root‐derived, aliphatic compounds were preferentially preserved in soil. Fresh wood additions elevated the amount of soil C recovered as light fraction material but also elevated mineralization during incubation compared with other DIRT treatments, suggesting that not all of the added soil C is directly stabilized. Aboveground needle litter additions, which are more N‐rich than wood debris, resulted in accelerated mineralization of previously stored soil carbon. In summary, our work demonstrates that the dominant plant sources of SOM differed substantially between forest types. Furthermore, inputs to and losses from soil C pools likely will not be altered uniformly by changes in litter input rates.
siRNA ET microRNA : BIOGENESE, MECANISME ET FONCTIONS

L’ARN interference est un mecanisme hautement conserve entre especes et permet d’eteindre l’expression d’un gene de maniere sequence specifique en utilisant un ARN double brin. Le role naturel du silencing par ARN semble etre la regulation fine des genes mais aussi dans la defense contre les elements transposables et les virus. La decouverte du mecanisme d’interference par l’ARN represente un saut majeur dans la recherche des genes cibles dans differentes maladies. Deux classes des petites molecules d’ARN ont ete trouvees comme etant des regulateurs sequence specifique posttranscriptionnelle : les siRNA et les microRNA (miRNA). Les siRNA sont produits a partir d’un double brin d’ARN qui est synthetise in vitro ou in vivo a partir des virus ou des sequences repetitives introduites par ingenierie genetique. Plusieurs miRNA endogenes sont programmes pour la regulation de l’expression des genes et ainsi participent a la croissance et le developpement de l’organisme. Les miRNA sont des importantes molecules regulatrices dans les plantes et les animaux
APPENDIX A: HEALTH RISK ASSESSMENT FOR THE NERVE AGENT GA

This Health Risk Assessment for the Nerve Agent GA is a draft report from September 1996 (editorial corrections made April 1997), prepared for the U.S. Department of the Army, Army Environmental Center under Interagency Agreement 1769-1769-A1, prepared by the Life Sciences Division of Oak Ridge National Laboratory (managed by Lockheed Martin Energy Research Corp. for the U.S. Department of Energy under contract DE-AC05-96OR22464), Oak Ridge, TN. It was submitted to the Material/ Chemical Risk Assessment Working Group Advisory and Coordinating Committee, Environmental Risk Assessment Program. This document is an internal review draft for review purposes only and does not constitute U.S. government policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.
Notes on breeding sites of Pelecaniformes in Micronesia

Summary During a tourist cruise with M.V. Academik Shokalski from Cairns (Australia) to Chuuk (Micronesia) between 20 March and 3 April 1996 we visited a number of seabird islands in Micronesia described by Nelson (1978). On these and other islands visited, we asked local people for further information on breeding seabirds. After the cruise H.M. visited Ant Atoll at Pohnpei. This note presents the results. Time did not allow us to undertake real counts so we provide only rough estimates of numbers of breeding pairs, in orders of magnitude.
Size-dependent mortality of juvenile Atlantic cod, estimated from recaptures of released reared cod and tagged wild cod

The recapture rate and survival of reared cod Gadus morhua L. (15–45 cm) released in fjords and open coastal areas of Norway increased with increasing size at release, while release area and season also had a significant influence on the results. High mortality soon after release reduced the number of released fish by more than two–thirds within 6 months, and reduced the potential commercial yield to a low level. In most cases the recapture yield was lower than the released biomass and the net yield increased little or not at all with increasing size at release. In western Norway high fishing mortality of young fish reduced the numbers of surviving fish rapidly and the growth overfishing reduced the potential yield still further. Natural mortality decreased with increasing size at release, and became low when the fish approached their size refuge, i.e. when they could not be eaten by their usual predators.
Optimizing wheat grain yield: effects of Rht (gibberellin-insensitive) dwarfing genes

Four sets of near-isogenic lines carrying different combinations of the alleles Rht-B1b, Rht-D1b and Rht-B1c for gibberellin-insensitive dwarfism in hexaploid wheat (Triticum aestivum L.) were compared with tall controls in a series of yield trials in eastern England and central Germany. In all four varietal backgrounds the effects of Rht-B1b and Rht-D1b were similar (plant height ≈ 86 and 83% of tall controls respectively) and in combination reduced plant height to c. 58%. The Rht-B1c allele caused more severe dwarfism (c. 50%) and, when combined with Rht-D1b, reduced plant height still further to c. 41%. Data from the trials were consistent with a model for height/yield relationships in which the pleiotropic effects of the Rht alleles on yield can be inferred from their primary function: insensitivity to gibberellin limits stem extension growth, decreasing assimilate demand for this organ and diverting it to the developing ear (which is not itself dwarfed). The net balance between the resulting increase in harvest index and the curvilinear relationship observed between plant height and total shoot yield results in optimum grain yields at intermediate plant heights. Yield advantages of shorter plants over tall controls were evident over several trials with mean grain yields ranging from 200 to 760 g m−2. The optimum plant height for yield improvement in different genetic backgrounds was achieved by different Rht alleles according to the background varietal height, such that intrinsically taller genotypes required more potent Rht alleles to achieve maximum potential grain yield. Ear yield components showed increases in grain number due to Rht pleiotropy, from which it is inferred that the number of grains per ear is limited by supply of assimilates pre-anthesis. Increases in grain number were associated with decreases in mean weight per grain which varied according to severity of dwarfism and varietal background, so that the net effect on grain yield per ear was sometimes positive, sometimes negative, and sometimes neutral in different Rht/variety combinations.
Evolution of Endemic Sideritis (Lamiaceae) in Macaronesia: Insights from a Chloroplast DNA Restriction Site Analysis

Abstract Sideritis L. subgenus Marrubiastrum (Lamiaceae) comprises 24 species of Macaronesian endemic perennials. The constituent taxa encompass a wide array of life forms that have exploited all ecological zones present in the Macaronesian archipelagos of Madeira and the Canary Islands. Though recently revised, an explicit phylogeny of the subgenus is still lacking. This group is especially intriguing because it exhibits the largest aneuploid series ever reported in oceanic island plants. The present study uses a chloroplast DNA restriction site analysis to elucidate the pattern of evolution within and among the islands. The insular taxa form a strongly supported monophyletic group, indicating a single colonization of Macaronesia. Monophyly of the sections is not supported. Integrating geographical and ecological distribution with the cpDNA phylogeny reveals a pattern of diversification within the islands consistent with adaptive radiation. Most other Macaronesian plant groups studied thus far have diversified by inter-island colonization between similar ecological zones. An analysis of chromosome number suggests a bimodal pattern of chromosomal change in the island subgenus, with one clade showing a decreasing aneuploid series and a second clade exhibiting aneuploid increase. The rate of change appears markedly amplified relative to that of the continental subgenus. This extreme level of chromosomal diversity stands in stark contrast to a general pattern of chromosomal stasis in island plants. Communicating Editor: John V. Freudenstein
Prevalence of Campylobacter foetus and Trichomonas foetus among cattle from Southern Africa

Trichomoniasis and campylobacteriosis are diseases caused by Trichomonas foetus and Campylobacter foetus respectively. These diseases pose economic losses due to infertility and abortion. The aim of this retrospective study was to estimate the prevalence of C. foetus and T. foetus among southern African cattle. Sheath washings and scrapings were subjected to polymerase chain reaction (PCR) for diagnosis of these microorganisms. Out of 3, 458 samples that were tested for T. foetus , 142 (4.1%) were positive. Campylobacter foetus was detected in 60 of the 3, 161 (1.9%) samples. The use of PCR was convenient for estimating the prevalence of C. foetus and T. foetus. Key words : Species-specific PCR, diagnosis, venereal disease, Campylobacter foetus, Trichomonas foetus.
EFEITO DE INSETICIDAS NA SEMEADURA SOBRE PRAGAS INICIAIS E PRODUTIVIDADE DE MILHO SAFRINHA EM PLANTIO DIRETO (1)

EFFECT OF INSETICIDES AT SOWING ON SEEDLING PESTS AND YIELD OFF-SEASON MAIZE CROP UNDER NO-TILLAGE SYSTEM Due to an increasing pest diversity in maize crop during the off-season, two autumn-winter experiments were conducted in the Medium Paranapanema region, State of Sao Paulo, Brazil, designated as Fields A and B, both in Cândido Mota County. The aim of the experiments were to evaluate the effect of insecticides on the control of pests occurring in the initial plant development. Treatments were the recommended dosage of the insecticides thiamethoxam (Cruiser 700 WS), carbofuran (Furazin 310 TS), imidacloprid (Gaucho FS), imidacloprid (Gaucho FS) + carbofuran (Furazin 310 TS), fipronil (Regent 800
Planting and tending productivity comparison in mounds and disc trenches using containerized and bareroot coniferous seedlings

In 2016 more then 40,300 ha of forest was regenerated in Latvia, where 13,000 ha were seeded or planted and 30,300 ha were left in natural regeneration. Before planting, usually one of two soil preparation methods are used – mounding or disc trenching. In areas with optimal water regime, disc trenching is used, while in wet areas mounding is used. Tree planting and after planting tending is done manually by hand tools. The aim of the study was to compare planting and tending productivity in different soil preparation methods (mounding and disc trenching) by planting different stocktypes (containerized and bareroot seedlings). Planting time studies were done in 12 sites and tending time studies in 8 sites. In planting time studies, different planting operations were measured and compared. In tending time studies, GPS devices were used, where area, distance and working time (productive and rest) was counted from GPS data. Average planting time for containerized seedlings in disc trenches was 10.3 seconds, while in mounds 9.2 seconds per seedling, an 11% improvement. Average planting time for bareroot seedlings in mounds was 28.3 seconds, while in trenches – 18.2 seconds, a 35% improvement. Tending in trenches was done faster than in mounds. On average, one hectare tending time in mounds was 8.4 hours, while in trenches 7.4 hours, an 11% improvement. Walked distance for 1 hectare tending in mounds was 5.4 km, 7% shorter than the distance of 5.0 km in trenches. Factors that influence planting and tending productivity are soil preparation quality, logging residue, and water level on the site. Data from planting and tending time studies could be used for better plan work activities and select suitable planting material for a particular soil preparation method.
Species and synonym list of the German marine macroalgae based on historical and recent records Arten- und Synomliste der Makroalgen in den Deutschen Küstengewässern - Auswertung von historischen und rezenten Befunden

A summary of all macroalgal records to occur in the German water bodies of the North Sea and the Baltic Sea during the last 190 years are presented, with their synonymes. All available literature and herbarium collections were revised and a potential species list was compiled. Therefore, the list reflects the sum of all records between 1819 and 2008 and not the actual presence of macroalgae along the German coast. 469 species have been recorded since 1819 including insecure registrations and single observations. Species richness decreases rapidly from the subtidal areas and the rocky shore of Helgoland to the brackish waters of the Baltic Sea with its often instable sediments. 322 species have been registered for Helgoland whereas the Western and Eastern part of the German Baltic Sea does not contain more than 211 and 181 species respectively. For the North Frisian Wadden Sea and the East Frisian Wadden Sea, 113 and 112 species have been registered, respectively. In relation to species number red algae are most abundant around the island of Helgoland, followed by brown and green algae. In the Frisian Wadden Sea green algae are most common, whereas in the Baltic Sea filamentous brown algae gain in importance. The presence of neophytes increased during the last decades, but total number does not exceed 10 species. The red algae Callithamnion teragonum, Halurus flosculosus and Neosiphonia harveyi are the latest new species records from Helgoland whereas Gracilaria vermiculophylla is the latest new species recorded in the German Wadden Sea and the Baltic Sea since 2004.