gebhart/patrepeval huggingface dataset:
Scalable Bayesian phylogenetics (2022)

Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain Monte Carlo (MCMC) sampling. Specifically, we discuss methods to improve the speed of likelihood calculations, reduce MCMC burn-in, and generate better MCMC proposals. We apply several of these techniques to study the evolution of HIV virulence along a 1536-tip phylogeny and estimate the internal node heights of a 1000-tip SARS-CoV-2 phylogenetic tree in order to illustrate the speed-up of such analyses using current state-of-the-art approaches. We conclude our review with a discussion of promising alternatives to MCMC that approximate the phylogenetic posterior. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
Coal Gasification in a Transport Reactor (2001)

An advanced transport reactor gasifier was operated using three different coals: Illinois #6 bituminous, Wyodak Powder River Basin subbituminous, and a Sufco Utah bituminous coals. A steady-state model was developed to evaluate the relative contributions of coal combustion and gasification of coal/char in this high-throughput reactor. The tests employed in-bed calcium-based sorbent for sulfur capture. The model was based on elemental mass and energy balances and assumed instantaneous devolatilization and combustion and kinetically limited gasification reactions in a continuously stirred tank reactor. The experimental results on the reaction of these three coals were compared with model predictions. The simulated results compared favorably with the experimental results (e.g., gas composition, carbon conversion, and reactor temperature). The bituminous coal data were accurately simulated as substoichiometric combustion processes. The more reactive subbituminous coal exhibited significant gasification conversion over the operating conditions tested. The subbituminous coal was found to react 20 times faster than reported from laboratory kinetic studies. The model was used to predict the performance of the gasifier, including the carbon conversion, sulfur capture, and composition and flow rate of product gas, based on operating conditions and input streams. Sensitivity studies on the coal feed rate, steam/coal ratio, heat loss, pressure, gas velocity, and coal reactivity were conducted. These simulations were used to compare the response of coals gasified to those combusted substoichiometrically, to evaluate the optimum operating conditions and to predict the performance in larger-scale units with less heat loss.
Enhanced oil recovery using CO sub 2 flooding (1990)

This patent describes an improvement in a method for recovering oil from an underground oil-bearing earth formation penetrated by an injection well and a producing well, in which method CO{sub 2} is injected into the formation to displace oil towards the producing well from which oil is produced to the surface. The improvement comprises injecting into the formation CO{sub 2}, the viscosity of which is increased at least three-fold by the presence of a sufficient amount of a polymer and a sufficient amount of a cosolvent to form a solution of the polymer in the CO{sub 2}.
Supplementary Table S2 from Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance (2023)

&lt;p&gt;Table S2. Liquid Chromatography and Mass Spectrometry Measurement of 2-hydroxyglutarate in the Conditioned Media of mIDH1 GCCs untreated, treated with vehicle (DMSO), or mIDH1 inhibitor (AGI-5198 or DS1001b)&lt;/p&gt;
Distribution of urease producing bacteria in the t I . r raDDlt caecum (1983)

The distributiono f urease-producinbga cteriaw as examinedi n lumenal and mucosal-associatedp opulationso f the rabbit caecum.T he total numbero f bacteriar ecoveredo n a nonspecific, s emi-definedm edium were 1,7 x 10ep er g from lumen contents and 2,0 x 10sp er g of washed,h omogenizedc aecal wall. Urease activity was shown by 5,3% of strains isolated from lumen contents and 21,770m ucosal-associateds trains. A higher proportion of bacteria associated with the caecal wall (63%) were facultative compared with 20% from the caecalcontent. Die verspreidingv an bakterie€w at ureasep roduseeri s onder' soek in die buisholtee n slymvliesg eassosieerdep opulasies van die konyn se sakderm. Die totale aantal bakteried wat her' win is op 'n nie-spesifiekes,e mi-gedefinieerdme edium was 1,7 x 10e per g van die buisholte inhoud en 2,0 x 105 per g van gewas en gehomogeniseerdesa kdermwand.U reasea ktiwiteit is aangetoon vir 5,370 van die stamme geisoleer uit die buisholte inhoud en 21,7oh van die slymvlies geassosieerde stamme. 'n Groter gedeelte van die bakterie€ wat geassosieer word met die sakdermwand (63%) was fakulatief in vergelyking met die 20o/ov a'fid ie sakdermi nhoud. Keywords : Urease, rabbit caecum, anaerobic bacteria, mucosalassociated flora
A simple micro-culture method for the study of group B arboviruses. (1969)

Thirty-nine group B arboviruses have been titrated by a simple micro-culture method. The technique uses a stable line of pig kidney cells (PS cells) in which plaques develop when cells are first infected in suspension in the wells of haemagglutination trays and are then incubated for from 3 to 10 days under an overlay containing carboxymethyl-cellulose. This method can be adapted to measure neutralizing antibodies, and the principle underlying the test is applicable to other cells and other viruses.
Monte Carlo simulation of a cobalt‐60 beam (1987)

We have used the Stanford Electron Gamma Shower (EGS) Monte Carlo code to compute photon spectra from an AECL Theratron 780 cobalt-60 unit. Particular attention has been paid to the careful modeling of the geometry and material construction of the cobalt-60 source capsule, source housing, and collimator assembly. From our simulation, we conclude that the observed increase in output of the machine with increasing field size is caused by scattered photons from the primary definer and the adjustable collimator. We have also used the generated photon spectra as input to a pencil beam model to calculate the tissue-air ratios in water and compared it to a model which uses a monochromatic photon energy of 1.25 MeV.
Pharmacological treatment and risk of psychiatric hospital admission in bipolar disorder (2017)

<b>Background</b>Clinical trials have examined the efficacy of drugs to prevent relapse in patients with bipolar disorder, however, their design often limits generalisation to routine clinical practice.<b>Aims</b>To estimate the effectiveness of drugs used for maintenance treatment in bipolar disorder.<b>Method</b>We used national registers to identify 35 022 individuals diagnosed with bipolar disorder and information on lithium, valproate, carbamazepine, lamotrigine, quetiapine and olanzapine treatment from 2006 to 2009. The main outcome was psychiatric hospital admissions. We used stratified cox regression to compare periods on and off medication within the same individual.<b>Results</b>Medication with lithium, valproate, lamotrigine, olanzapine and quetiapine was associated with reduced rates of admission to hospital. Lithium was more effective than quetiapine and olanzapine. The effects of specific drugs depended on the polarity of the mood episode.<b>Conclusions</b>Our findings complement results from randomised controlled trails, but suggest that lithium is more effective than both quetiapine and olanzapine in routine clinical practice.
Hydrogels: Glacier Moraine Formation‐Mimicking Colloidal Particle Assembly in Microchanneled, Bioactive Hydrogel for Guided Vascular Network Construction (Adv. Healthcare Mater. 2/2015) (2015)

On page 195 J. Lee, H. J. Kong, and colleagues demonstrate a new method to align microparticles releasing bioactive molecules in microchannels of a hydrogel, allowing the guiding of growth direction and spacing of vascular networks.
Novel and Efficient Method for Esterification, Amidation Between Carboxylic Acids and Equimolar Amounts of Alcohols, and Amines Utilizing Me2NSO2Cl and N,N‐Dimethylamines; Its Application to the Synthesis of Coumaperine (XII), a Natural Chemopreventive Dieneamide. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Artificial intelligence: Deep learning in oncological radiomics and challenges of interpretability and data harmonization (2021)

Over the last decade there has been an extensive evolution in the Artificial Intelligence (AI) field. Modern radiation oncology is based on the exploitation of advanced computational methods aiming to personalization and high diagnostic and therapeutic precision. The quantity of the available imaging data and the increased developments of Machine Learning (ML), particularly Deep Learning (DL), triggered the research on uncovering "hidden" biomarkers and quantitative features from anatomical and functional medical images. Deep Neural Networks (DNN) have achieved outstanding performance and broad implementation in image processing tasks. Lately, DNNs have been considered for radiomics and their potentials for explainable AI (XAI) may help classification and prediction in clinical practice. However, most of them are using limited datasets and lack generalized applicability. In this study we review the basics of radiomics feature extraction, DNNs in image analysis, and major interpretability methods that help enable explainable AI. Furthermore, we discuss the crucial requirement of multicenter recruitment of large datasets, increasing the biomarkers variability, so as to establish the potential clinical value of radiomics and the development of robust explainable AI models.
Novel Flexible Triboelectric Nanogenerator based on Metallized Porous PDMS and Parylene C (2020)

Triboelectric nanogenerators (TENGs) have recently become a powerful technology for energy harvesting and self-powered sensor networks. One of their main advantages is the possibility to employ a wide range of materials, especially for fabricating inexpensive and easy-to-use devices. This paper reports the fabrication and preliminary characterization of a novel flexible triboelectric nanogenerator which could be employed for driving future low power consumption wearable devices. The proposed TENG is a single-electrode device operating in contact-separation mode for applications in low-frequency energy harvesting from intermittent tapping loads involving the human body, such as finger or hand tapping. The novelty of the device lies in the choice of materials: it is based on a combination of a polysiloxane elastomer and a poly (para-xylylene). In particular, the TENG is composed, sequentially, of a poly (dimethylsiloxane) (PDMS) substrate which was made porous and rough with a steam-curing step; then, a metallization layer with titanium and gold, deposited on the PDMS surface with an optimal substrate–electrode adhesion. Finally, the metallized structure was coated with a thin film of parylene C serving as friction layer. This material provides excellent conformability and high charge-retaining capability, playing a crucial role in the triboelectric process; it also makes the device suitable for employment in harsh, wet environments owing to its inertness and barrier properties. Preliminary performance tests were conducted by measuring the open-circuit voltage and power density under finger tapping (~2 N) at ~5 Hz. The device exhibited a peak-to-peak voltage of 1.6 V and power density peak of 2.24 mW/m2 at ~0.4 MΩ. The proposed TENG demonstrated ease of process, simplicity, cost-effectiveness, and flexibility.
Head-tracking and subject positioning using binaural headset microphones and common modulation anchor sources (2004)

A prerequisite in many systems for virtual and augmented reality audio is the tracking of a subject's head position and direction. When the subject is wearing binaural headset microphones, the signals from them can be cross-correlated with known sound sources, called here anchor sources, to obtain an accurate estimate of the subject's position and orientation. In this paper we propose a method where the anchor sources radiate in separate frequency bands but with common modulation signal. After demodulation, distance estimates between anchor sources and binaural microphones are obtained from positions of cross-correlation maxima, which further yield the desired head coordinates. A particularly attractive case is to use high carrier frequencies where disturbing environment noise is lower and sensitivity of hearing to detect annoying anchor sources is also lower.
Inhibition of IgE synthesis by anti-IgE: role in long-term inhibition of IgE synthesis by neonatally administered soluble IgE. (1990)

Inoculation of syngeneic IgE into 2- to 12-day-old mice results in prolonged synthesis of anti-IgE antibodies without further challenge. These anti-IgE antibodies may be largely responsible for the long-term inhibition of synthesis of IgE that is known to result from a perinatal challenge with IgE. This conclusion is supported by the effect of passive inoculation of syngeneic polyclonal anti-IgE antibodies into young mice, which similarly results in selective inhibition of IgE synthesis. Further evidence is the close relationship between the age dependency of IgE-induced inhibition of subsequent IgE synthesis and the ability of IgE to induce anti-IgE antibodies. IgE synthesis was monitored at the level of secretion by B cells as well as serum IgE levels and IgE antibody responses.
Genes Involved in the Astrocyte-Neuron Lactate Shuttle (ANLS) Are Specifically Regulated in Cortical Astrocytes Following Sleep Deprivation in Mice (2013)

This study shows that TSD induces the expression of genes associated with ANLS specifically in astrocytes, underlying the important role of astrocytes in the maintenance of the neuro-metabolic coupling across the sleep-wake cycle.
A Systematic Nomenclature for Codifying Engineered Nanostructures (2009)

Nanotechnology's growing applications are fueled by the synthesis and engineering of a myriad nanostructures, yet there is no systematic naming or classification scheme for such materials. This lack of a coherent nomenclature is confusing the interpretation of data sets and threatens to hamper the pace of progress and risk assessment. A systematic nomenclature that encodes the overall composition, size, shape, core and ligand chemistry, and solubility of nanostructures is presented. A typographic string of minimalist field codes facilitates digital archiving and searches for desired properties. This nomenclature system could also be used for nanomaterial hazard labeling.
New tools in an old trade: CS1 pilus morphogenesis (1998)

CS1 pili serve as the prototype for a large class of serologically distinct pili associated with enterotoxigenic Escherichia coli that cause diarrhoea in humans. The four genes essential for CS1 pilus morphogenesis, cooB, A, C and D, are arranged in an operon and encode structural and assembly proteins unlike those of other pilus systems commonly associated with Gram-negative bacteria. CS1 pili are composed primarily of the major pilin subunit, CooA, which determines the serological type of the pilus. The major pilin subunit is assembled into pili by the proteins CooB, CooC and CooD. CooD is both a minor component found at the pilus tip and an essential assembly protein, whereas CooC is an outer membrane protein thought to be involved in pilin transport. CooB is a novel periplasmic chaperone-like protein that forms intermolecular complexes with and stabilizes the major and minor pilins. Unlike other pilin chaperones, CooB also stabilizes the outer membrane component of the assembly system, CooC. The proteins of CS1 pili have no significant homology to those of the well-characterized Pap (pyelonephritis-associated) pili and related systems, although most of the features of pilus morphogenesis are similar. Therefore, these appear to be among the rare cases of convergent evolution. Thus, for CS1 pili, enterotoxigenic E. coli use new protein 'tools' in the old 'trade' of forming functional pili.
Nitric oxide (NO) photo-release in a series of ruthenium–nitrosyl complexes: new experimental insights in the search for a comprehensive mechanism (2018)

The mechanism of nitric oxide release is investigated along a series of 1–3 “push–pull” ruthenium nitrosyl complexes.
Undergraduate Biology Instructors Still Use Mostly Teacher-Centered Discourse Even When Teaching with Active Learning Strategies (2020)

Abstract Reform efforts in undergraduate science, technology, engineering, and mathematics (STEM) instruction often emphasize student-centered teaching approaches, but relatively little attention is paid to the way STEM teachers use discourse when interacting with their students. In the present study, we examined the instructional and discourse behaviors of biology faculty members (N = 20) teaching in undergraduate biology classes. Although we found that the biology teachers spent most of their time guiding student learning in active learning activities and less time presenting, an analysis of their classroom communicative approaches showed that the participants mostly used authoritative and not dialogic discourse to teach biology content. Similarly, we found a strong positive correlation between biology teachers guiding student learning and authoritative, interactive approaches, suggesting that these teachers mostly asked the students to recall facts or basic concepts rather than asking them to collaboratively build knowledge. We describe the implications of these findings and our results for undergraduate biology instruction.
Supplementary Table 2 from Baseline Peripheral Blood Biomarkers Associated with Clinical Outcome of Advanced Melanoma Patients Treated with Ipilimumab (2023)

&lt;p&gt;Spectrum of factors, cut-offs, and differences in overall survival according to biomarkers in the identification and the confirmation cohort. Absolute (Abs.), Relative (Rel.), Lactate dehydrogenase (LDH), regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs). * Green characters indicate the category associated with better survival in the identification cohort. ** Green cells indicate significant differences in overall survival (p &lt; 0.05). Red cells indicate non-significant findings.&lt;/p&gt;
von Willebrand disease update: diagnostic and treatment dilemmas (2008)

Although von Willebrand disease (VWD) is now well-described, many facets of diagnosis and management continue to be debated. The diagnosis of type 1 disease can be difficult but recent genetic analyses help to distinguish many factors which can influence von Willebrand factor (VWF) levels and bleeding phenotype. Type 2 disease (functional abnormalities) includes a particularly interesting group of disorders with faulty binding between VWF and FVIIIC (Normandy) where treatment methods need careful consideration. Type 3 VWD is the most severe form of VWD and a new international study is underway to examine the use of prophylaxis.
Electronic structure ofPbSe∕PbScore-shell quantum dots (2007)

The electronic structure of $\mathrm{Pb}\mathrm{Se}∕\mathrm{Pb}\mathrm{S}$ core-shell quantum dots (QDs) is calculated within a four-band envelope function formalism. The effective mass approximation used successfully to model PbS and PbSe core QDs is extended to include discontinuities in material parameters. The model shows that even though $\mathrm{Pb}\mathrm{Se}∕\mathrm{Pb}\mathrm{S}$ is a type-II heterostructure, for typical quantum dot sizes type-II properties will not be observed. Instead, the wave functions are predicted to extend throughout both materials. Experimental results confirm the unique properties of these nanostructures.
Adaptive Randomized Study of Idarubicin and Cytarabine Versus Troxacitabine and Cytarabine Versus Troxacitabine and Idarubicin in Untreated Patients 50 Years or Older With Adverse Karyotype Acute Myeloid Leukemia (2003)

Neither troxacitabine combination was superior to IA in elderly patients with previously untreated adverse karyotype AML.
Comparison of new triton X-100- and tween-ether-treated split-treated vaccines in children (1981)

Split-product vaccines (SPVs) combine the desirable properties of no systemic reactogenicity and adequate immunogenicity when two doses are given. We compared a new Triton X-100 SPV (Connaught Laboratories, Inc.) with the commercially available Tween-ether SPV (Parke-Davis & Co.) in 76 children and young adults 2 to 25 years old; there were 39 and 37, respectively, in each vaccine group. Both vaccines contained influenza A/Brazil/78, A/Texas/77, and B/Hong Kong/72 (7 microgram of hemagglutinin for each strain); two doses were administered 1 month apart. Among persons seronegative by the hemagglutination inhibition test, the geometric mean antibody titers rose to approximately 100 after the first vaccination for influenza A/Brazil/78 and A/Texas/77. For B/Hong Kong/72, however, seronegative recipients developed lower geometric mean titers of approximately 32 after one immunization. Against the new B/Singapore/79 strain neither SPV stimulated adequate cross-reacting hemagglutination inhibition antibody (geometric mean titers of approximately 10). In conclusion, the new Triton X-100 SPV appears to be comparable to the ether-treated SPV in primed subjects. Further studies in unprimed children should be done to confirm this impression. In addition, it would be advisable to study other dosage regimens in unprimed children with these SPVs.
Kinetic studies of the reactions of BrO and IO radicals (1997)

The 193‐nm laser photolysis Of Br 2 /N 2 O mixtures in N 2 buffer has been utilized to determine the absorption cross section of BrO and to study the reactions of O( 3 P ) with Br 2 , O( 3 P ) with BrO, and the self reaction of BrO at room temperature. The measured kinetic data are in good agreement with the literature values. Molecular bromine formation in the self‐reaction of BrO can be described by the concerted steps of Br+BrO→BrOBr and Br+BrOBr→Br 2 +BrO. From a curve fitting of the simultaneously monitored BrO and IO decays in the Br 2 /I 2 /N 2 O system, room temperature rate constants for the BrO+IO→Products and I+BrO→IO+Br reactions of (6.9±2.7)×10 −11 cm 3 /molecule/s and (1.2±0.6)×10 −11 cm 3 molecule/s, respectively, were derived. Similar experiments using IBr, instead of Br 2 /I 2 , revealed a marked sensitivity of the rate constant analysis to the accessible ratio of radical concentrations. Kinetic analysis of this complex reaction system is presented.
A Retrospective Analysis of Skin Bacterial Colonisation, Susceptibility and Resistance in Atopic Dermatitis and Impetigo Patients (2015)

Atopic dermatitis (AD) and impetigo are skin conditions where bacterial colonisation and infection, especially with Staphylococcus aureus play an important role. We compared skin bacterial population, resistance patterns and choice of antimicrobial agents in patients diagnosed with AD and impetigo during 2005 and 2011 in our department. Number of positive cultures in the AD group were 40 and 53 in 2005 and 2011, with S. aureus found in 97.5% and 100%, respectively. Differences in resistance were marginal. In impetigo, S. aureus was found in all 70 patients in 2005 and all 40 patients in 2011. Antibiotic resistance to specifically fusidic acid was more common in 2005 impetigo patients (22.8%) versus 2011 (5%) (p = 0.078). The most commonly used oral antimicrobial was cefadroxil (in 57.5% and 52.8% of AD and 58.6% and 35% of impetigo patients in 2005 and 2011, respectively). Our observations confirm the high prevalence of S. aureus in both diseases and, interestingly, show a declining resistance trend in impetigo.