Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of the preconfigured Varian Ethos Acuros XB Beam Model for treatment planning dose calculations: A dosimetric study

Abstract Varian (Palo Alto, California, United States) recently released an online adaptation treatment platform, Ethos, which has introduced a new Dose Preview and Automated Plan Generation module despite sharing identical beam data with the existing Halcyon linac. The module incorporates a preconfigured beam model and the Acuros XB algorithm (Ethos AXB model) to generate final dose calculations from an initial fluence optimization. In this study, we comprehensively validated the accuracy of the Ethos AXB model by comparing it against the Halcyon AXB model, the Halcyon Anisotropic Analytical Algorithm (AAA) model, and measurements acquired on an Ethos linac. Results indicated that the Ethos AXB model demonstrated a comparable if not superior dosimetric accuracy to the Halcyon AXB model in basic and complex calculations, and at the same time its dosimetric accuracy in modulated and heterogeneous plans was better than that of the Halcyon AAA model. Despite the fact that the same algorithm was utilized, the Ethos AXB model and the Halcyon AXB model still exhibited variations across a range of tests, although these variations were predominantly insignificant in the clinical environment. The accuracy of the Ethos AXB model has been successfully verified in this study and is considered appropriate for the current clinical scope. On the basis of this study, clinical physicists can perform a data validation instead of a full data commissioning when implementing the Ethos system, thereby adopting a more efficient approach for Ethos installation.
Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.
A new species of genus Anteaglonium (Anteagloniaceae, Pleosporales) with its asexual morph

The family Anteagloniaceae comprises the genera, Anteaglonium and Flammeascoma. The family shares similar characters with taxa in the Hysteriales, but groups in the Pleosporales. No asexual morph is known in this family. In the present study we introduce a new species Anteaglonium thailandicum , re-examine A. parvulum and document its asexual morph . We observed different culture characters with similar morphology and molecular data for four strains of A. parvulum isolated from collections in Thailand . In this study we introduce A. thailandicum which has different hysterothecial characters as compared to A. parvulum and A. globosum , especially in the globose, roughened wall, indistinct slit, short subicula and short tomentum and also based on differences in LSU, SSU and TEF sequence data.
Morphological, Agronomical, Phenological and Stand Persistence Traits of Some Wild Narrowleaf Birdsfoot Trefoil (Lotus tenuis Waldst. & Kit.) Populations

Existing information on the ecology, distribution and plant traits of Lotus taxa is scant for the natural flora of Turkey, which is one of the most important countries in the Mediterranean zone for genetic resources and genetic diversity of these species. Therefore, the aim of this study was to determine (i) morphologic, agronomic, phenologic, stand persistence traits and growth habits of some wild narrowleaf birdsfoot trefoil (NBT; Lotus tenuis Waldst. & Kit.), and (ii) the relationships between these traits and altitude, latitude or longitude of the natural habitats, the samples of which were obtained from diverse natural areas of Black Sea Region, Turkey. The altitudes of sampling sites ranged from 1 to 1510 m. A total of 86 wild NBT were sampled in the study. NBT was present in all ranges of altitude, although its frequency was the highest in altitudes between 1-300 m. On the other hand, considerable variations were determined for the investigated traits, except for growth habit in which all populations had decumbent growth habit. The results of the present study indicate that NBT better adapted to lowlands and studied region offers important genetic resources for further researches and also may serve as a valuable breeding material for new grazing-type and disease resistant NBT varieties.
Primer Notes

We have developed primers for detecting allelic variation at several microsatellite loci using the polymerase chain reaction (PCR) in the snow crab Chionoecetes opilio and we evaluated their utility in other crab species. A size-selected genomic library was constructed using a DNA mix extracted from the pereopods of 20 unrelated C. opilio females following a standard lysis and proteolysis with SDS (sodium dodecyl sulphate) and proteinase K (Sambrook et al. 1989). Pooled DNA was digested with MboI, subjected to agarose electrophoresis and fragments ranging from 300 to 1000 bp were isolated using the GENECLEAN II kit (Bio/Can Scientific). These fragments were cloned into the BamHI site of pUC18 using 400 ng of size-selected DNA and 200 ng of plasmid DNA in a total volume of 20 μL, following a standard ligation reaction according to Sambrook et al. (1989). Five μL of the ligation mixture were used to transform Escherichia coli DH5α by electroporation according to the method of Dower et al. (1988). Approximately 5 × 10 recombinant clones were obtained and screened for microsatellites using (CA)10, (CAC)5, and (GACA)4 probes. Hybridizations were carried out according to Ali et al. (1986). A total of 186 positive clones were isolated, of which 54 were analysed by sequencing reactions on alkaline-denatured plasmid DNA by the dideoxynucleotide chain-termination method (Sanger et al. 1977) with T7 polymerase (Pharmacia). Primers were designed for six loci using OLIGOTEST V-2.0 (Beroud et al. 1990) and are summarized in Table 1. PCR reactions were carried out in a Perkin-Elmer/Cetus DNA thermal cycler (model N801–0150) with one of the primers end-labelled with [γ-P]-dCTP and using 5–100 ng of genomic DNA in a 12.5 μL total volume (Bowcock et al. 1993), with 1.6 μM of each primer, 0.25 U of Taq DNA polymerase (Pharmacia), 200 μM of each dNTP, and 10× PCR buffer supplied with the Taq DNA polymerase. The PCR conditions were: denaturation for 1 min at 94 °C, annealing for 1 min at the temperatures specified in Table 1, and extension for 1 min at 72 °C for 25–30 cycles. PCR products were resolved by electrophoresis on 6–8% denaturing polyacrylamide gels. The gels were dried and exposed at Molecular Ecology (1998) 7, 357–363
A false traumatic aneurysm of the superficial temporal artery: case report and literature review

Introduction: Pseudoaneurysms or false aneurysms originating from superficial temporal artery (STA) are rare and often seen as facial swellings. These forms of aneurysms often involve the intimal and media layers of the arterial wall. So far only single cases have been reported at various locations across the world since 1644. We report another unique case of traumatic STA pseudoaneurysms. Case Presentation: We present a 51-year-old man with a 1-year history of a pulsatile mass on the left forehead. He suffered a blunt trauma at the temporal region of the left forehead a year prior. Computed tomography angiography confirmed left STA pseudoaneurysms. The lesion was total resected via surgery. We reconstructed parent artery after resecting the pseudoaneurysm. The patient recovered well with an overall good cosmetic look. Conclusions: It is very necessary to report the occurrences of STA pseudoaneurysms because the swelling could be mistaken for other lesions leading to inappropriate treatment especially in facilities with no modern radiologic modalities.
Counts and Estimates of Taxonomic Abundance in Faunal Remains: Microtine Rodents from Bluefish Cave I

Widely advertised theoretical and methodological deficiencies in counts of identi- fied specimens (NISP) and the minimum number of individuals (MNI) have prompted a search for alternate methods of estimating taxonomic abundance in faunal remains. Most proposed alternatives have merely represented modifica- tions or "refinements" of the MNI count outlined by Theodore White thirty years ago (White 1953). Modifications by Chaplin (1971) and Krantz (1968) are exam- ined in this paper. Recently, an alternative, based on the Peterson index, has been proposed by Fieller and Turner (1982). Based on capture-recapture techniques used in the biological sciences, the Peterson index is superior to other proposed methods, because it is statistically well founded on the hypergeometric distribu- tion and can be framed by data-based confidence intervals. Despite these advan- tages, the actual use of this estimate is limited by a number of practical exigencies that will undoubtedly force zooarchaeologists to continue to use NISP and MNI counts as abundance measurements of last resort. The assumptions and require- ments for the use of the Peterson index, and the "behaviour" of this variable as compared with NISP and the methods of White, Chaplin, and Krantz, are illustrated with microtine rodent data from Bluefish Cave I, northern Yukon Territory.
Genetic Correlations Among Field Trials of Norway Spruce Clones Representing Different Propagation Cycles

Abstract Serial cutting propagation means that clones are produced in consecutive propagation cycles, where a new round of cuttings are taken from the previously rooted cuttings, etc. The objective of this study was to judge the importance of propagation cycle on height growth in field trials. In a field trial series with Norway spruce clones, comprising nine trials in four cutting propagation cycles, propagation cycle only had a minor effect on height growth compared to the site effect. For inter-site correlation models where all trials were included, the best fit was obtained by an unstructured model, while the most parsimonious model included constraints on the correlations depending on cycle structure. Model constraints based on grouping of the trials by site productivity did not improve the fit. Testing for generally good performers over a range of different site conditions appears to be a good approach, unless drivers of genotype by environment interaction can be identified.
Optimization of cytochrome C oxidase subunit I gene amplification primers for eight kinds of rodents in I nner Mongolia

Objective To determine the optimal primers of cytochrome C oxidase subunit I (CO I) gene for 8 kinds of rodents in natural epidemic focus of plague in Inner Mongolia. Methods In Xilingol League and Wulanchabu City of Inner Mongolia, eight kinds of rodents were collected and DNA was extracted; six pairs of targeted primers (F1/R1, F2/R2, F3/R3, F4/R4, VF/VR, F6/R6) were used to amplify the CO I gene of the 8 species by PCR; PCR products were send to biotechnology company for sequencing, and bioinformatics analysis of the sequencing results was conducted. Results F3/R3 was the optimal CO I gene primer for Spermophilus dauricus; cocktail primer (VF/VR) was the optimal CO I gene primer for Ochotona daurica and Lagurus przewalskii; F6/R6 was the optimal CO I gene primer for Rhombomys opimus, Phodopus campbelli and Microtus brandti; F2/R2 was the optimal CO I gene primer for Allactaga sibirica, and F1/R1 was the optimal CO I gene primer for Meriones meridianus. CO I gene sequences of the 8 kinds of rodents were compared; DNA barcoding was unique in each rodent and every rodent had differential point. Conclusions Different rodent needs its own species-specific primers for CO I gene amplification. Upon amplification of different rodent, cocktail or F6/R6 primers are the first choices, and choose the species-specific primers for particular species to amplify. Key words: Plague; Gene amplification; DNA primer
Limitaciones físicas y químicas de la digestibilidad de pastos tropicales y estrategias para aumentarla

The high fiber content in tropical forages, and its limited digestion by ruminants, is one of the greatest limitations to adequate animal productivity in the tropics. The discussion in this paper focuses in two areas: The first relates to voluntary intake by grazing rumi­nants, the factors that affect it and practical methods to increase intake in grazing or high-fiber consuming ruminants. For the value of discussion, it must be recognized that although assessment of voluntary intake of confined animals is not complicated, estimations of intake by grazing animals have been traditionally difficult and often imprecise. The implementation of pasture renovation strategies, the use of mixed (grass – legume) swards and of strategic supple­mentation, have often been reported as suc­cessful methods to increase voluntary intake by grazing ruminants. The second area of discussion relates to fiber digestibility in ruminants and includes comments on practi­cal ways to increase rumen fiber degrad­ability. Both areas are highly related with each other, and adequate understanding and management of factors that affect these two processes is needed to ensure the economic and environmental sustainability of cattle production in the tropics.
Functional Quantitative Genetics and the Missing Heritability Problem

Functional Quantitative Genetics and the Missing Heritability Problem Serge Sverdlov Chair of the Supervisory Committee: Professor Elizabeth A. Thompson Department of Statistics In classical quantitative genetics, the correlation between the phenotypes of individuals with unknown genotypes and a known pedigree relationship is expressed in terms of probabilities of IBD states. In existing models of the inverse problem where genotypes are observed but pedigree relationships are not, probabilities and correlations have either a Bayesian or a hybrid interpretation. We introduce the IBF (Identity by Function) model based on the classic infinite allele mutation process. Describing genetic resemblance in terms of functional states defines a genetic architecture for a trait without reference to specific alleles or a population, treating a gene-scale functional region, rather than a SNP, as a QTL, and emphasizing locus weights and patterns of dominance over multiple alleles. This allows the reconciliation of bottom-up (genome sequence based) and (pedigree/population) calculations of heritability, as well as phenotype and gene effect prediction. We perform these calculations with simulated, pig, and human traits. For related computational problems, we describe an algorithm for the estimation in large scale variance components problems by matrix decomposition methods techniques related to the Sparse Bayesian Learning/Relevance Vector Machine framework. Additionally, we describe a combinatorial framework for decomposing nonlinear genetic effects due to dominance and epistasis, and a method for adjusting the Genomic Relationship Matrix for linkage disequilibrium by SNP selection and weighting.
inhibition shrimp melanosis (black spot) by ficin

Melanosis of pink shrimp (Penaeus duorarum) was significantly inhibited by treatment with dilute solutions of the sulfhydryl protease ficin. The ficin was effective as a substitute for sulfites in preventing black spot formation under refrigerated storage of more than 1 week. The mode of action of ficin is presumed to be inhibition of the polyphenol oxidase enzyme (PPO) responsible for the shrimp melanosis
Male disguised females: costs and benefits of female‐limited dimorphism in a butterfly

1. In polymorphic species, two or more discrete phenotypes co‐occur simultaneously. Sex‐limited polymorphism is a particular case of polymorphism, in which several discrete morphs coexist within one of the two sexes only. Several hypotheses were proposed to explain the existence and the maintenance of sex‐limited polymorphism in insects: (i) the morphs have similar fitness, such as similar survival and expected fecundity, and their frequencies vary randomly (i.e. the null hypothesis); (ii) harassment by males is reduced towards the less common female morph, in this case andromorph females (i.e. the male mimicry and learned mate recognition hypotheses); (iii) morphs differ in predation risk (i.e. the predation hypothesis); or (iv) morphs differ in thermoregulation ability (i.e. the thermoregulation hypothesis).
Association of age and cause-special mortality in patients with stage I/ II colon cancer: A population-based competing risk analysis

Purpose This study aimed to determine the probability and prognostic factors of colon cancer-specific mortality (CCSM) and noncancer-specific mortality (NCSM) for patients with stage I/II colon cancer and evaluate the association of age on cause-specific mortality. Materials and methods From Surveillance, Epidemiology, and End Results (SEER) database, we identified 33152 patients with stage I/II colon cancer undergoing surgery between 2004 and 2011. The cumulative incidence of CCSM and NCSM was calculated, and competing risk analysis was performed to investigate prognostic factors for cause-specific mortality. Results In patients <50, 50–75, and >75 years of age, 5-year cumulative incidence of CCSM was 5.7%, 7.8%, and 16.1%, respectively (overall, 10.6%); 5-year cumulative incidence of NCSM was 2.2%, 7.1%, and 26.9%, respectively (overall, 13.8%). The probability of CCSM and NCSM increased with advanced age. The 5-year cumulative incidence of CCSM was higher than NCSM in patients <50 years of age, whereas lower in patients >75 years of age. The probability of CCSM and NCSM was similar in patients 50–75 years of age. Competing-risk multivariable analysis demonstrated that increasing age was a strong predictor of CCSM (per year increase, SHR 1.03,95% confidence interval [CI]: 1.03–1.04). Age was most predictive of NCSM: (per year increase, SHR 1.08, 95% CI: 1.08–1.08). Conclusion Age was significantly associated with an increased cumulative incidence of CCSM and NCSM of patients with stage I/II colon cancer underwent surgery. NCSM was a significant competing event and should be adequately considered when performing survival analysis.
Astrocytes in the Ventrolateral Preoptic Area Promote Sleep

Although ventrolateral preoptic (VLPO) nucleus is regarded as a center for sleep promotion, the exact mechanisms underlying the sleep regulation are unknown. Here, we used optogenetic tools to identify the key roles of VLPO astrocytes in sleep promotion. Optogenetic stimulation of VLPO astrocytes increased sleep duration in the active phase in naturally sleep-waking adult male rats (n = 6); it also increased the extracellular ATP concentration (n = 3) and c-Fos expression (n = 3–4) in neurons within the VLPO. In vivo microdialysis analyses revealed an increase in the activity of VLPO astrocytes and ATP levels during sleep states (n = 4). Moreover, metabolic inhibition of VLPO astrocytes reduced ATP levels (n = 4) and diminished sleep duration (n = 4). We further show that tissue-nonspecific alkaline phosphatase (TNAP), an ATP-degrading enzyme, plays a key role in mediating the somnogenic effects of ATP released from astrocytes (n = 5). An appropriate sample size for all experiments was based on statistical power calculations. Our results, taken together, indicate that astrocyte-derived ATP may be hydrolyzed into adenosine by TNAP, which may in turn act on VLPO neurons to promote sleep. SIGNIFICANCE STATEMENT Glia have recently been at the forefront of neuroscience research. Emerging evidence illustrates that astrocytes, the most abundant glial cell type, are the functional determinants for fates of neurons and other glial cells in the central nervous system. In this study, we newly identified the pivotal role of hypothalamic ventrolateral preoptic (VLPO) astrocytes in the sleep regulation, and provide novel insights into the mechanisms underlying the astrocyte-mediated sleep regulation.
The General Concept of a Neo‑Institutional Causal Sphere in Company Management

Background. The general concept of a neo‑institutional causal sphere was devel‑ oped in response to the question about what company management, understood as practice, is from the perspective of dynamic changes taking place in a broadly defined coherent causal sphere. A critical analysis of the literature on new institutional economics, psychology, and sociology, observation of the socio‑economic reality, and the author’s long experience in managing companies became the prime movers behind the formulation of the concept presented in this paper. Research aims. As a result of the search for answers to the key question, two hypotheses emerged. The first one concerns understanding a company as a collection of activities in the form of socio‑economic phenomena, whereas the other is related to human activity within a company, which shapes the neo‑institutional manufacturing system. It is a process of the direct achievement of the organization’s objectives using appropriate tools. However, the most important subject here is the contracting man. In this context, the author of the article proposes a thesis according to which company management practice, as defined by the neo‑institutional perspective, should be oriented towards broad‑aspect determinism of a coherent causal sphere. Methodology. In order to support his thesis, the author first presents issues con‑ cerning a company from the neo‑institutional perspective, providing a background for the concept of a coherent causal sphere. The second part of the paper discusses a coherent causal sphere identified with the dynamic environment of a company. And finally, the author defines functions of company management in the context of a coherent causal sphere, which have a chance of forming a new direction in modern company management. Key
Cloning and characterization of Xenopus b2-microglobulin

cDNAs for Xenopus b2-microglobulin (b2m), the obligatory light chain of most vertebrate Major Histocompatibility Complex (MHC) class I molecules, were isolated and ESTs were identified. Alignment of the deduced amino acid sequence to other species’ b2m showed that the overall structure is evolutionarily conserved, and phylogenetic analysis showed that the Xenopus b2m sequence is intermediate between fish and bird/mammal b2m. The Xenopus b2m mRNA is expressed ubiquitously with highest expression in intestine, spleen, and thymus, correlating well with classical class Ia expression. b2m mRNA and protein were also detected in Xenopus thymic tumor and kidney cell lines. Segregation analysis on a tetraploid Xenopus laevis family revealed two independently segregating, non-MHC-linked loci. As expected, only one locus was found in the diploid Xenopus tropicalis, strongly suggesting that the two b2m loci in the tetraploid species were generated by genomewide duplication, and did not undergo diploidization unlike many other MHC genes. q 2005 Elsevier Ltd. All rights reserved.