gebhart/patrepeval huggingface dataset:
Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol (2014)

The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut.
Nematic colloidal micro-robots as physically intelligent systems (2022)

Physically intelligent micro-robotic systems exploit information embedded in micro-robots, their colloidal cargo, and their milieu to interact, assemble and form functional structures. Nonlinear anisotropic fluids like nematic liquid crystals (NLCs) provide untapped opportunities to embed interactions via their topological defects, complex elastic responses, and their ability to dramatically restructure in dynamic settings. Here we design and fabricate a 4-armed ferromagnetic micro-robot to embed and dynamically reconfigure information in the nematic director field, generating a suite of physical interactions for cargo manipulation. The micro-robot shape and surface chemistry are designed to generate a nemato-elastic energy landscape in the domain that defines multiple modes of emergent, bottom-up interactions with passive colloids. Micro-robot rotation expands the ability to sculpt interactions; the energy landscape around a rotating micro-robot is dynamically reconfigured by complex far-from-equilibrium dynamics of the micro-robot's companion topological defect. These defect dynamics allow transient information to be programmed into the domain and exploited for top-down cargo manipulation. We demonstrate robust micro-robotic manipulation strategies that exploit these diverse modes of nemato-elastic interaction to achieve cargo docking, transport, release, and assembly of complex reconfigurable structures at multi-stable sites. Such structures are of great interest to future developments of LC-based advanced optical device and micro-manufacturing in anisotropic environments.
Pb‐free solder bumping for flip chip package by electroplating (2003)

Sn‐Pb and Sn‐Ag bumps (130 μ m diameter, 250 μ m pitch) made using an electroplating process were studied. As a preliminary experiment, the effects of current density and plating time on the Sn‐Pb and Sn‐Ag deposits were investigated. The morphology and composition of the plated surface were examined using scanning electron microscopy. The shape and thickness of the solder bumps were also compared. Bump shear testing was performed to measure the adhesion strength between the solder bumps and the under bump metallurgy. In electroplating, the Sn‐Ag plating thickness was proportional to the current density, while plated Sn‐Pb thickness saturated above the limiting current density. The optimal conditions for solder bump fabrication were found at 6 A/dm 2 for 3 h in the case of Sn‐Pb bump plating and 6 A/dm 2 for 1 h for the Sn‐Ag bump plating. The bump shear strength for Sn‐Ag was found to be higher than that of Sn‐Pb.
Level of agreement between 2002 American–European Consensus Group and 2012 American College of Rheumatology classification criteria for Sjögren’s syndrome and reasons for discrepancies (2014)

Agreement was only moderate between ACR and AECG criteria, suggesting these two sets would not select comparable patient populations. An international consensus about which classification criteria should be used in clinical studies is needed.
Pattern recognition based on time-frequency analysis and convolutional neural networks for vibrational events in φ-OTDR (2018)

Based on vibration signals detected by a phase-sensitive optical time-domain reflectometer distributed optical fiber sensing system, this paper presents an implement of time-frequency analysis and convolutional neural network (CNN), used to classify different types of vibrational events. First, spectral subtraction and the short-time Fourier transform are used to enhance time-frequency features of vibration signals and transform different types of vibration signals into spectrograms, which are input to the CNN for automatic feature extraction and classification. Finally, by replacing the soft-max layer in the CNN with a multiclass support vector machine, the performance of the classifier is enhanced. Experiments show that after using this method to process 4000 vibration signal samples generated by four different vibration events, namely, digging, walking, vehicles passing, and damaging, the recognition rates of vibration events are over 90%. The experimental results prove that this method can automatically make an effective feature selection and greatly improve the classification accuracy of vibrational events in distributed optical fiber sensing systems.
Histone Deacetylase Inhibitor Trichostatin A Represses Estrogen Receptor α-Dependent Transcription and Promotes Proteasomal Degradation of Cyclin D1 in Human Breast Carcinoma Cell Lines (2004)

Tamoxifen has been shown to inhibit ERalpha-mediated cyclin D1 transcription, and acquired resistance to tamoxifen is associated with a shift to ERalpha-independent cyclin D1 up-regulation. Taken together, our data show that TSA effectively induces cyclin D1 down-regulation through both ERalpha-dependent and ERalpha-independent mechanisms, providing an important new strategy for combating resistance to antiestrogens.
Super-hydrophobic surfaces of layer-by-layer structured film-coated electrospun nanofibrous membranes (2007)

We have recently fabricated super-hydrophobic membrane surfaces based on the inspiration of self-cleaning silver ragwort leaves. This biomimetic super-hydrophobic surface was composed of fluoroalkylsilane (FAS)-modified layer-by-layer (LBL) structured film-coated electrospun nanofibrous membranes. The rough fibre surface caused by the electrostatic LBL coating of TiO2 nanoparticles and poly(acrylic acid) (PAA) was used to imitate the rough surface of nanosized grooves along the silver ragwort leaf fibre axis. The results showed that the FAS modification was the key process for increasing the surface hydrophobicity of the fibrous membranes. Additionally, the dependence of the hydrophobicity of the membrane surfaces upon the number of LBL coating bilayers was affected by the membrane surface roughness. Moreover, x-ray photoelectron spectroscopy (XPS) results further indicated that the surface of LBL film-coated fibres absorbed more fluoro groups than the fibre surface without the LBL coating. A (TiO2/PAA)10 film-coated cellulose acetate nanofibrous membrane with FAS surface modification showed the highest water contact angle of 162° and lowest water-roll angle of 2°.
Changes in cyclic nucleotide levels and dimorphic transition in Candida albicans (1980)

The relationship between the levels of cyclic nucleotides and dimorphic transition in Candida albicans was examined. The results showed that cells of this pathogenic fungus contained both cyclic adenosine 3',5'-monophosphate (cAMP) and cyclic guanosine 3',5'-monophosphate (cGMP), the concentration of the latter being about one-tenth that of the former in stationary-phase cells of the yeast form. Our results further indicated that germ tube formation induced by incubation at 40 degrees C followed a rise in cAMP concentration in the cell with no accompanying change in cGMP content. Cysteine, which suppressed germination, also reversed the increase in intracellular cAMP concentration. Dibutyryl cAMP (1 MM) significantly promoted germination in proline medium at temperatures of 32 to 34 degrees C. These results suggested that cAMP was one of the controlling factors in the morphological transition in Candida albicans.
Projektmanagement (2014)

ZusammenfassungDer Zweck von Wirtschaftsunternehmen ist die Leistungserstellung und -vermarktung. In der Regel erfolgt dies in sich wiederholenden, standardisierten Routineprozessen, der so genannten Linienarbeit. Die Linienorganisation von Unternehmen ist auf diese Arbeiten zugeschnitten. Ihre Ausgestaltung zielt auf Optimierung (Arbeitsteilung und Spezialisierung) bekannter Aufgaben und eingespielter Arbeitsweisen, um ein marktgerechtes Kostenniveau zu erhalten. Neben den Routinearbeiten sind jedoch Innovationsprozesse für den langfristigen Erfolg eines Unternehmens unabdingbar. Für immer mehr Firmen werden innovative Vorhaben sogar zur Alltagsaufgabe.
Neo-Republicanism as a Route to Animal Non-Domination (2016)

In this article, we reinterpret the current political turn in animal rights theory in terms of republican as opposed to liberal political theory. By appealing to the values of liberty and fraternity as well as equality, we argue for a conception of animal liberation from human domination and not from humanity per se. This establishes a basis of liberty and fraternity in our cooperative relationships with animals in a "zoopolis," or interspecies political community. We contend that such a basis for interspecies political cooperation is not available on the more traditional model of animal liberation, where rights are derived from weak equality of the species.
Community structure and scale-free collections of Erdős-Rényi graphs (2012)

Community structure plays a significant role in the analysis of social networks and similar graphs, yet this structure is little understood and not well captured by most models. We formally define a community to be a subgraph that is internally highly connected and has no deeper substructure. We use tools of combinatorics to show that any such community must contain a dense Erdős-Rényi (ER) subgraph. Based on mathematical arguments, we hypothesize that any graph with a heavy-tailed degree distribution and community structure must contain a scale-free collection of dense ER subgraphs. These theoretical observations corroborate well with empirical evidence. From this, we propose the Block Two-Level Erdős-Rényi (BTER) model, and demonstrate that it accurately captures the observable properties of many real-world social networks.
Preparation, Characterization, and FET Properties of Novel Dicyanopyrazinoquinoxaline Derivatives (2004)

[structure: see text] A series of the title dicyanopyrazinoquinoxaline derivatives have been prepared and characterized by using single-crystal X-ray structure analysis and redox potential measurements. They have strong electron-accepting properties due to the pyrazinopyrazine skeletons as well as the cyano groups. Substituents can be easily introduced at the benzene ring and control the HOMO-LUMO energy gap and the molecular packing. They show clear n-type transistor properties in the FET devices.
Email classification for Spam Detection using Word Stemming (2010)

Unsolicited emails, known as spam, are one of the fast growing and costly problems associated with the Internet today. Among the many proposed solutions, a technique using Bayesian filtering is considered as the most effective weapon against spam. Bayesian filtering works by evaluating the probability of different words appearing in legitimate and spam mails and then classifying them based on that probabilities.Most of the current spam email detection systems use keywords to detect spam emails.These keywords can be written as misspellings eg: baank or bannk instead of bank. Misspellings are changed from time to time and hence spam email detection system needs to constantly update the blacklist to detect spam emails containing misspellings. It"s impossible to predict all possible misspellings for a given keyword and add those to the blacklist. In this paper a better and more successful approach for improving E-mail content classification for spam control is proposed. It used the Word Stemming or Word Hashing Technique for improving the efficiency of the content based spam filter.The proposed system extract the base or stem of a misspelled or modified word, to detect spam emails. It considers every misspelled keyword applies a word stemming technique and passes the base word to the content based filter. Using a proposed if-then rule, we can decide whether or not this unknown mail is spam
Genomics-driven precision medicine for advanced pancreatic ductal carcinoma (PDAC): Early results from the COMPASS trial (NCT02750657). (2018)

211 Background: COMPASS is a prospective study with the primary aim to identify predictive mutational and transcriptional features in advanced PDAC for improved patient stratification and treatment selection. Methods: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy for whole genome sequencing (WGS) and RNA sequencing (RNASeq). Fresh tumor tissue was acquired by image guided percutaneous core needle biopsy of locally advanced primary or metastatic tumors. Laser capture microdissection was performed for all cases to ensure high-resolution genomic analyses. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures. Results: Of 63 patients who underwent a tumor biopsy between December 2015 and June 2017, WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range 19-52 days) from biopsy, meeting the primary feasibility endpoint. Three patients with an ‘unstable’ genomic subtype, including two with a novel ‘duplicator’ phenotype, responded well to m-FOLFIRINOX. Of two cases with the same germline BRCA2 mutation, only the chemotherapy responder had loss of heterozygosity and genomic hallmarks of double stranded break repair deficiency. Approximately 25% of tumors displayed the basal-like RNA expression signature and these were chemotherapy resistant, with tumor shrinkage mainly observed in those with the classical RNA subtype (P = 0.003). Thirty percent of patients had potentially actionable genetic alterations. Conclusions: Prospective comprehensive genomic profiling of advanced PDAC is feasible and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtypes providing the impetus for further studies. Clinical trial information: NCT02750657.
Formation and characterization of thin films of H(CH <sub>2</sub> ) <sub> <i>x</i> </sub> PO(OH) <sub>2</sub> on polycrystalline zinc substrates (2002)

Abstract Monolayers of n ‐pentanephosphonic or n ‐tetradecanephosponic acids are obtained by immersion of mechanically polished zinc substrates in solutions of either absolute ethanol or a mixture of water/ethanol (25/75%). X‐ray photoelectron spectroscopy, contact angle and scanning Kelvin probe measurements indicate that both compounds lead to good‐quality monolayers and the longer alkyl chain n ‐tetradecanephosponic acid molecules form the more densely packed films. However, the best films ( n ‐tetradecanephosponic acids) do not show any resistance to electrochemical assays (polarization curves in NaOH and NaCl). Copyright © 2002 John Wiley & Sons, Ltd.
Lithocholic acid in human liver: Identification of ∈‐lithocholyl lysine in tissue protein (1977)

Abstract Human liver had been shown to contain two forms of lithocholic acid. One form is extractable by 95% ethanol‐ammonia, 1000∶1, v/v (soluble lithocholate, SL) and the other form is firmly bound to the tissue residue. The latter, tissue‐bound lithocholic acid (TBL), can be enzymatically released by means of the specific clostridial peptide bond hydrolase, cholylglycine hydrolase (cholanoyl amino acid hydrolase, EC no. 3.5). Solvolytic procedures for the analysis of hepatic lithocholic acid sulfate revealed that almost all of the TBL was non sulfated, while in the SL fraction there was an apparent preponderance of the sulfated form. Cholylglycine hydrolase liberates free labeled lithocholic acid from synthetic [24‐ 14 C] lithocholyl‐bovine serum albumin and from [24‐ 14 C]lithocholyl polylysine. By analogy, the enzyme releases lithocholic acid from tissue protein in which the bile acid is conjugated through amino groups of basic side chains. Hydrolysis of [24‐ 14 C] lithocholyl polylysine with 6n HC1 yielded ∈‐[24‐ 14 C] lithocholyl lysine, which was chromatographically similar to the product obtained by acid hydrolysis of TBL. Chromatographic, infrared, and mass spectroscopic studies with synthetic N‐α‐lithocholyl lysine, N‐∈‐lithocholyl lysine, and N‐α‐∈‐Bis lithocholyl lysine showed the hydrolytic product from TBL to be N‐∈‐lithocholyl lysine. Since monohydroxy bile acids, such as lithocholic acid, are known to show unusual cytotoxic properties, the identification of TBL in human liver poses important questions regarding the role of lithocholate in liver injury.
Sulfur dioxide emissions during the 2011 eruption of Shinmoedake volcano, Japan (2013)

Sulfur dioxide flux of the 2011 Shinmoedake eruption, which started in January 2011, was measured repeatedly throughout its activity. The SO2 flux, which was greater than 10,000 ton/day during the earlier stages, quickly decreased to below 1,000 ton/day over the following two weeks. The flux decreased gradually thereafter to about 200 ton/day by the second half of March 2011. It continued at that level until April 2012. To evaluate the amount of SO2 emitted during the 2011 eruption, daily SO2 flux was estimated based on direct observations and other information. The total SO2 emissions were about 280 kt, with nearly two-thirds emitted during the first two weeks. The degrees of excess degassing estimated for the lava accumulation stages were low (2.3–2.9), suggesting a small pre-eruptive bubble content in the magma. High SO2 flux observed immediately after the sub-Plinian eruptions and before rapid lava effusion is probably related to the extensive degassing of magma in the conduit, which probably played a role in the transition from explosive to effusive eruption. An abrupt and large flux decrease occurred around February 8, 2011, which might be attributable to depletion of pre-eruptive bubbles in the magma.
Nanodrähte, Nanosägen, Nanospiralen. Eindimensionale Materialien aus Halbleitern (2005)

Die Synthese von Halbleiter-Nanodrähten beruht auf Verdampfung und Rekondensation des Materials. Die Nanodrähte entstehen auf dem Substrat, wenn dieses mit einem vorstrukturierten Katalysator beschichtet ist. Während der Synthese löst sich das Halbleitermaterial im geschmolzenen Katalysatortröpfchen und lagert sich zum Substrat hin als feste Phase ab: Unter dem Tröpfchen wächst das Nanoröhrchen als Einkristall heran. Aus dem Dampf kann sich weiteres Halbleitermaterial anlagern und so eine große Formenvielfalt hervorbringen. Nanodrähte lassen sich gezielt mit Fremdatomen dotieren. Das eröffnet viele zukünftige Anwendungsmöglichkeiten in der Hableitertechnologie.
Use of a yeast site-specific recombinase to produce female germline chimeras in Drosophila. (1992)

We describe an efficient method for generating female germline mosaics by inducing site-specific homologous mitotic recombination with a yeast recombinase (FLP) which is driven by a heat shock promoter. These germline mosaics are produced in flies heterozygous for the agametic, germline-dependent, dominant female sterile (DFS) mutation ovoD1, where only flies possessing germline clones are able to lay eggs. This method, the "FLP-DFS" technique, is very efficient because more than 90% of females with germline clones can be recovered. We show that this heat-inducible, site-specific mitotic recombination system does not affect viability and that the germline clones recovered are physiologically the same as those created by X-ray induced mitotic recombination. We describe the parameters of FLP-recombinase induced germline mitotic recombination and the use of the "FLP-DFS" technique to analyze the maternal effect of X-linked zygotic lethal mutations.
5.12 Tb/s (128 × 42.7 Gb/s) Transmission with 0.8 bit/s/Hz Spectral Efficiency over 1280 km of Standard Single-Mode Fiber Using All-Raman Amplification and Strong Signal Filtering (2002)

All-Raman transmission of 128times42.7 Gb/s at 50 GHz channel spacing over 1280 km of standard single-mode fiber is demonstrated. This record capacity for this high spectral efficiency is achieved by strong filtering of carrier-suppressed return-to-zero signals
Interindividual Variability in Stress Susceptibility: A Role for Epigenetic Mechanisms in PTSD (2013)

Post-traumatic stress disorder (PTSD) is a psychiatric condition characterized by intrusive and persistent memories of a psychologically traumatic event that leads to significant functional and social impairment in affected individuals. The molecular bases underlying persistent outcomes of a transient traumatic event have remained elusive for many years, but recent studies in rodents have implicated epigenetic modifications of chromatin structure and DNA methylation as fundamental mechanisms for the induction and stabilization of fear memory. In addition to mediating adaptations to traumatic events that ultimately cause PTSD, epigenetic mechanisms are also involved in establishing individual differences in PTSD risk and resilience by mediating long-lasting effects of genes and early environment on adult function and behavior. In this review, we discuss the current evidence for epigenetic regulation of PTSD in human studies and in animal models and comment on ways in which these models can be expanded. In addition, we identify key outstanding questions in the study of epigenetic mechanisms of PTSD in the context of rapidly evolving technologies that are constantly updating and adjusting our understanding of epigenetic modifications and their functional roles. Finally, we discuss the potential application of epigenetic approaches in identifying markers of risk and resilience that can be utilized to promote early intervention and develop therapeutic strategies to combat PTSD after symptom onset.
A neural network clustering algorithm for the ATLAS silicon pixel detector (2014)

A novel technique to identify and split clusters created by multiple charged particles in the ATLAS pixel detector using a set of artificial neural networks is presented. Such merged clusters are a common feature of tracks originating from highly energetic objects, such as jets. Neural networks are trained using Monte Carlo samples produced with a detailed detector simulation. This technique replaces the former clustering approach based on a connected component analysis and charge interpolation. The performance of the neural network splitting technique is quantified using data from proton-proton collisions at the LHC collected by the ATLAS detector in 2011 and from Monte Carlo simulations. This technique reduces the number of clusters shared between tracks in highly energetic jets by up to a factor of three. It also provides more precise position and error estimates of the clusters in both the transverse and longitudinal impact parameter resolution.