gebhart/patrepeval huggingface dataset:
Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes (2022)

Abstract Host genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiont Saccharimonadaceae . Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.
Exploring Audiovisual Support Systems for In-Car Multiparty Conferencing (2019)

Calling while driving poses a severe safety risk. When more than two people are involved in a call - a conference call - this risk increases even more. Intelligent vehicles could offer support systems that ease the cognitive burden of such a multiparty calls. We explore the possibilities of such advanced driving assistant systems (ADAS) in two ways: first, we investigate object-based spatial audio where each remote caller is modeled as a distinct audio source. Second, we apply a non-intrusive ambient stereoscopic 3D (S3D) visualization that indicates the current speaker and its location. In a between-subject design driving simulator study (n=56), we assess workload, user experience and driving performance. Surprisingly, we found no positive effect of object-based audio. However, we present evidence how a supporting visualization might lower situational stress and increase the system’s dependability. We conclude that a supportive and intelligent stereoscopic visualization is a promising candidate for enhancing multiparty conference calls while driving.
Preferential Rearrangements of the VγI Subgroup of the γ‐Chain of the T‐Cell Antigen Receptor to Jγ2Cγ2 Gene Segments in Peripheral Blood Lymphocyte Transcripts from Normal Donors (1993)

To investigate whether there are preferential VJC gene rearrangements of the gamma-chain of the human T-cell antigen receptor (TCR), we amplified and sequenced gamma-chain TCR transcripts from peripheral blood lymphocytes from adult normal donors. cDNA was synthesized from total RNA and amplified by the polymerase chain reaction (PCR) using 5' primers specific for either the V gamma I or the V gamma II subgroups of the gamma-chain of the TCR. The amplified cDNAs were then cloned and sequenced. The majority (approximately 83%) of the cDNAs employing V-I subgroup gene segments rearranged to J gamma 2 (J gamma 2.1 or J gamma 2.3) C gamma 2 gene segments. This was in contrast to the predominant rearrangement of the V gamma II subgroup (V gamma 9) to J gamma 1.2C gamma 1. The remaining 13% of the cDNAs employing V gamma I subgroup gene segments rearranged to J gamma 1.1C gamma 1 or J gamma 1.3C gamma 1. There was significant N diversity as well as imprecise joining at the VJ junction. gamma delta TCR utilizing the C gamma 1 gene segment are disulfide-linked, whereas those utilizing the C gamma 2 gene segment are non-disulfide-linked. These results demonstrate that peripheral blood gamma-chain transcripts exhibit preferential rearrangements of V gamma I subgroup gene segments to J gamma 2(2.1,2.3)C gamma 2 gene segments. By contrast, V gamma II subgroup (V gamma 9) transcripts exhibit rearrangements to J gamma 1.2C gamma 1.
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology (2023)

Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
Anti-GM-CSF Monoclonal Antibody Therapy for Refractory Acute Leukemia (1998)

Several phase I trials and pilot studies using Monoclonal Antibody (MoAb) have been performed in B-cell neoplasms, but this approach has not until now been extensively tested in myeloid leukemias. Recently, we evaluated the use of anti-Granulocyte-Macrophage Colony-Stimulating Factor MoAb (Anti-GM-CSF MoAb) in acute myeloid leukemia (AML). Eight patients fulfilled inclusion criteria and received a single course of Anti-GM-CSF MoAb infusion during 5 to 15 days. Anti-GM-CSF MoAb was well tolerated and was detectable in pharmacokinetics studies. Using Human Anti-Rat Antibodies (HARA), we also observed an immunological response to the MoAb. Despite sufficient levels detected in the serum and biological activity of Anti-GM-CSF MoAb in vivo, no anti-leukemic effect was noted, except for one patient who had a decrease of 50% in the marrow blast cell mass. These observations indicate that leukemic proliferation in vivo involves a complex network spanning many mechanisms, and inhibition of leukemia is not effective if only one of these key targets is attacked. The development of these new approaches may be more effective in the future.
Filament‐Based Melt Electrowriting Enables Dual‐Mode Additive Manufacturing for Multiscale Constructs (2023)

Melt electrowriting (MEW) is an electric-field-assisted fiber-forming biofabrication strategy for the additive manufacturing (AM) of precisely defined 3D microarchitectures. MEW is based on pressure-driven extrusion of a polymer melt pool, currently mainly implemented at laboratory scale with specialized machine technology and limited to only few materials. This precludes the accessibility of MEW to a broader user group and can become the bottleneck of MEW's technological advancement. In contrast to conventional MEW, a filament-based approach (F-MEW) is introduced that exploits the technological ecosystem of fused filament fabrication (FFF), a globally used transformative AM technique. In this work, a polymer filament serves as feedstock material and is melted just on demand. By upgrading existing FFF systems, MEW of polymer microfibers is enabled, as validated with polycaprolactone (PCL) and demonstrated with direct writing of thermosensitive polydioxanone (PDO). Finally, FFF and F-MEW are hybridized in a dual-mode AM process. This enables multiscale constructs featuring both FFF struts and one order of magnitude smaller F-MEW microfibers. This work opens the accessibility of F-MEW to the large FFF user group, potentially benefitting from the plethora of filaments available for FFF, while, at the same time, expanding the FFF fabrication window.
Experimental Measurement of the Divergent Quantum Metric of an Exceptional Point (2021)

The geometry of Hamiltonian's eigenstates is encoded in the quantum geometric tensor (QGT), containing both the Berry curvature, central to the description of topological matter, and the quantum metric. So far, the full QGT has been measured only in Hermitian systems, where the role of the quantum metric is mostly limited to corrections. On the contrary, in non-Hermitian systems, and, in particular, near exceptional points, the quantum metric is expected to diverge and to often play a dominant role, for example, in the enhanced sensing and in wave packet dynamics. In this Letter, we report the first experimental measurement of the quantum metric in a non-Hermitian system. The specific platform under study is an organic microcavity with exciton-polariton eigenstates, which demonstrate exceptional points. We measure the quantum metric's divergence, and we determine the scaling exponent n=-1.01±0.08, which is in agreement with the theoretical description of second-order exceptional points.
Novel Space-Time Adaptive Processing Methods for Gaussian and Non-Gaussian Radar Clutter (2001)

Our work on this contract has four main thrusts. We addressed (1) the problem of optimal target detection of a rank one signal in additive non-Gaussian clutter modeled as a spherically invariant random process. Performance analysis of the optimal signal processor was carried out. However, practical implementation of the optimal processor requires know- ledge of the probability density function underlying the clutter, which is often unavailable. Hence, (2) we considered the performance of sub-optimum as well as ad-hoc approximations to the optimal processor. Next, (3) we concerned ourselves with the performance of parametric space-time adaptive processing methods in Gaussian interference and addressed issues of detection probability. constant false alarm rate and reduced training data support. Finally, (4) we provided a rigorous statistical analysis of the recently proposed non-homogeneity detector, which is useful for training data selection in STAP applications.
Clinical Value of Crystalluria and Quantitative Morphoconstitutional Analysis of Urinary Calculi (2004)

Morphoconstitutional analysis of urinary calculi, i.e. morphologic examination combined with Fourier transform infrared spectroscopy (FTIR), is of decisive interest for the diagnosis of rare but severe inherited or acquired stone diseases such as cystine, 2,8-dihydroxyadenine, xanthine, struvite, ammonium urate or drug-containing calculi as well as primary hyperoxalurias. In the absence of early diagnosis and proper management, these diseases may lead to progressive loss of renal function. Among common forms of calcium oxalate (CaOx) stones, predominant CaOx monohydrate (whewellite) is mainly associated with hyperoxaluric conditions whereas predominant CaOx dihydrate (weddellite) is mainly associated with hypercalciuria, and this distinction is of interest to orient metabolic evaluation and preventive measures. Crystalluria examination, also based on morphology and FTIR, is a valuable diagnostic method when no stone is available for analysis. Presence of specific crystals (cystine, 2,8-dihydroxyadenine, struvite, ammonium urate) is diagnostic by itself. In all types of nephrolithiasis, serial crystalluria determination appears as a simple, cheap and reliable method to evaluate the risk of stone formation and assess the effectiveness of preventive measures. Determination of urinary crystal volume was in our experience a useful tool in the management of patients with cystinuria or primary hyperoxaluria in the post-transplantation period. In conclusion, both accurate morphologic and FTIR analysis of stones and serial crystalluria determination should be more largely used, in view of their value in the diagnosis and management of renal stone formers.
ChemInform Abstract: Acylation of Fluorocarbethoxy‐Substituted Ylids: A Simple and General Route to α‐Fluoro β‐Keto Esters. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Making Classifying Selectors Work for Foam Elimination in the Activated‐Sludge Process (2003)

Classifying selectors are used to control the population of foam-causing organisms in activated-sludge plants to prevent the development of nuisance foams. The term, classifying selector, refers to the physical mechanism by which these organisms are selected against; foam-causing organisms are enriched into the solids in the foam and their rapid removal controls their population at low levels in the mixed liquor. Foam-causing organisms are wasted "first" rather than accumulating on the surface of tanks and thereby being wasted "last", which is typical of the process. This concept originated in South Africa, where pilot studies showed that placement of a flotation tank for foam removal prior to secondary clarifiers would eliminate foam-causing organisms. It was later simplified in the United States by using the aeration in aeration tanks or aerated channels coupled with simple baffling and adjustable weirs to make continuous separation of nuisance organisms from the mixed liquor.
Emptiness Yoga. Jeffrey Hopkins. (1991)

Emptiness Yoga. Jeffrey Hopkins, Snow Lion, Ithaca, NY, 1987. pp. £13.50/$19.95.
Colloids and Colloid Assemblies: Synthesis, Modification, Organization and Utilization of Colloid Particles (2004)

Foreword.Preface.1. Latex Particles (Klaus Tauer).2. Semiconductor Nanoparticles (Andrey L. Rogach, Dmitri V. Talapin and Horst Weller).3. Monolayer Protected Clusters of Gold and Silver (Mathias Brust and Christopher J. Kiely).4. Sonochemical Synthesis of Inorganic and Organic Colloids (Franz Grieser and Muthupandian Ashokkumar).5. Colloidal Nanaoreactors and Nanocontainers (Marc Sauer and Wolfgang Meier).6. Miniemulsions for the Convenient Synthesis of Organic and Inorganic Nanoparticles and Single Molecule Applications in Materials Chemistry (Katharina Landfester and Markus Antonietti).7. Metal and Semiconductor Nanoparticle Modification via Chemical Reactions (Luis M. Liz Marzan).8. Nanoscale Particle Modification via Sequential Electrostatic Assembly (Frank Caruso).9. Colloidal Crystals: Recent Developments and Niche Applications (Younan Xia, Hiroshi Fudouzi, Yu Lu, and Yadong Yin).10. Surface-directed Colloids Patterning: Selective Deposition via Electrostatic and Secondary Interactions (Paula T. Hammond).11. Evolving Strategies of Nanomaterials Design (Sean Davis).12. Nanoparticle Organization at the Air-water Interface and in Langmuir-Blodgett Films (Murali Sastry).13. Layer-by-layer Self-assembly of Metal Nanaparticles on Planar Substrates: Fabrication and Properties (Thierry P. Cassagneau).14. Assembly of Electrically Functional Microstructures from Colloidal Particles (Orlin D. Velev).15. 3D Ordered Macroporous Materials (Rick C. Schroden and Andreas Stein).16. Semiconductor Quantum Dots as Multicolor and Ultrasensitive Biological Labels (Warren C.W. Chan, Xiaohu Gao and Shuming Nie).17. Colloids for Encoding Chemical Libraries: Applications in Biological Screening (Bronwyn J. Battersby, Lisbeth Grondahl, Gwendolyn A. Lawrie, and Matt Trau).18. Polyelectrolyte Microcapsules as Biomimetic Models (Gleb B. Sukhorukov and Helmuth Mohwald).Subject Index.
Fluctuating Lift Forces of the Karman Vortex Streets on Single Circular Cylinders and in Tube Bundles: Part 2—Lift Forces of Single Cylinders (1972)

The fluctuating lift force of the Karman vortex on a single circular cylinder will be investigated theoretically for an ideal inviscid vortex street with rectilinear vortices. In this investigation the model introduced by von Karman will be used. As a result, the relationship between the fluctuating lift coefficient CL and the characteristic dimensions of the vortex street can be derived. This leads to establishing the equation between the fluctuating lift coefficient CL and the steady pressure drag coefficient CD. Since the curve of the theoretical lift coefficient practically envelops the spreading field of the experimentally determined points, the theory can be considered to be adequate to give the right order of magnitude for the lift of the Karman vortex. It will further be shown, that the spread of the measured values is in connection with the correlation length of the vortex along the cylinder axis.
Distribution, 14C chronology, and paleomagnetism of latest Pleistocene and Holocene lava flows at Haleakalā volcano, Island of Maui, Hawai‘i: A revision of lava flow hazard zones (2006)

New mapping and 60 new radiocarbon ages define the age and distribution of latest Pleistocene and Holocene (past 13,000 years) lava flows at Haleakalā volcano, Island of Maui. Paleomagnetic directions were determined for 118 sites, of which 89 are in lava flows younger than 13,000 years. The paleomagnetic data, in conjunction with a reference paleosecular variation (PSV) curve for the Hawaiian Islands, are combined with our knowledge of age limitations based on stratigraphic control to refine age estimates for some of the undated lava flows. The resulting volumetric rate calculations indicate that within analytical error, the extrusion rate has remained nearly constant during the past 13,000 years, in the range 0.05–0.15 km 3 /kyr, only about half the long‐term rate required to produce the postshield strata emplaced in the past ∼1 Myr. Haleakalā's eruptive frequency is similar to that of Hualālai volcano on the Island of Hawai‘i, but its lava flows cover substantially less area per unit time. The reduced rates of lava coverage indicate a lower volcanic hazard than in similar zones at Hualālai.
A phase 1 trial of a human thymus-expressed apoptosis factor in patients with advanced solid tumors: Interim report. (2015)

e14018 Background: This apoptosis factor (NEROFE) is a 14-a.a. modified form of a hormone-like peptide present in the human thymus, which plays a key role in immune system regulation. In preclinical evaluation, it induced apoptosis in cancer cells, inhibited angiogenesis/metastasis, and showed in vivo efficacy with no toxicity. Methods: This ongoing, single-center, first-in-human, 3+3 dose-escalation study of this factor given I.V. at 6 mg/m2-96 mg/m2over 5 3-pt cohorts (3 times a week; 28-day cycle) examines the MTD, safety, PK profile, and anti-tumor activity in pts with advanced solid tumors. Pts undergo tumor assessments every other cycle. Samples for PK are taken on days 1 of cycles 1 and 2. Results: To date, 14 previously treated (57% ≥ 3 lines) and 1 first line pts (M = 8, F = 7, median age: 63) with advanced/metastatic solid tumors have been enrolled. MTD has not been reached. Treatment was well-tolerated with no cumulative toxicity. The most frequently observed AEs (G < 2) in the first 4 cohorts were: hypertension (21%) and increased bilirubin (14%); 5 of 15 evaluable pts continued therapy beyond cycle 2. SD was noted in 2 pts: colorectal cancer (6M) and spinal cord neoplasia (+10M). PK was dose-dependent and approximately linear (Table). Factor administration was associated with orders of magnitude decreases in plasma levels of VEGF A, PDGF AA, PDGF BB, VEGF D, bFGF, aFGF and Angiopoeitin-1 in all pts in cohorts 3 and 4. Also, in 3 pts with elevated plasma EGF levels, it decreased the levels to below normal levels. In the 2 pts that achieved SD, tumor biopsies stained positive to ST2 receptor, had increased plasma TNF-alpha and IL-2. Conclusions: This factor administered at doses up to 96 mg/m2is safe, well-tolerated, and demonstrates interesting anti-angiogenic activity in combination with increased immune cytokines. Tumor ST2 expression may be a biomarker for sensitivity to this factor. Dose-escalation continues in this trial. Clinical trial information: NCT01690741. PK Parameters Dose (mg/m2) Auc0-t (ng h/mL) Cmax (ng/ml) T1/2 (hrs) Cycle 1 Day 1 Cycle 2 Day 1 Cycle 1 Day 1 Cycle 2 Day 1 Cycle 1 Day 1 Cycle 2 Day 1 Cohort 1 6 3813 9719 1209 1536 2.3 2.8 Cohort 2 12 12905 11452 6048 6048 2.1 2.0 Cohort 3 24 49630 57069 14609 14609 3.2 3.7 Cohort 4 48 79935 100093 18267 22113 4.9 4.6
Cerament G vs. Bonealive putty in der Behandlung der (Infekt)-Pseudarthrose. Eine Gegenüberstellung beider Therapieverfahren am etablierten (Infekt)pseudarthrosenmodell der Ratte (2020)

Fragestellung Die erfolgreiche Behandlung von (Infekt)-pseudarthrosen stellt die Orthopädie und Unfallchirurgie bis heute vor große Herausforderungen. Meist sind mehrere Revisionsoperationen notwendig um eine knöcherne Konsolidierung und eine Eradikation der Infektsituation zu gewährleisten. Gerade bei größeren knöchernen Defeksituationen ist der Einsatz von Knochenersatzstoffen häufig notwendig. Allerdings ist es aufgrund des heterogenen Patientenspektrums kaum möglich unterschiedliche Knochenersatzsoffe in klinischen Studien miteinander zu vergleichen.
Functional Analysis of Grafts from Living Donors (1996)

Clinical recovery after a small-for-size transplant is characterized by significant functional impairment associated with paradoxical histologic changes typical of ischemia. These changes apparently are due to graft injury, which can only be the result of small graft size. These findings have significant implications for the extension of LRLT to adults.
Expedient Preparation of Aryllithium and Arylzinc Reagents from Aryl Chlorides Using Lithium 4,4′-Di-tert-Butylbiphenylide and Zinc(II) Chloride (2015)

We report an efficient method for the preparation of aryllithium and zinc reagents from inexpensive and readily available aryl chlorides by using lithium 4,4′-di-<i>tert</i>-butylbiphenylide (LiDBB) as a lithiation reagent. The resulting organometallic reagents underwent subsequent reactions with a variety of electrophiles, such as an aldehydes, DMF, PhSSO<sub>2</sub>Ph, TsCN, an aryl halide, or an acid chloride (through Pd-catalyzed cross-coupling). Aryl chlorides bearing substituents, including methoxy, 3,4-methylenedioxy, fluoride, TMS, OTMS, NMe<sub>2</sub>, acetal, and ketal, were shown to be appropriate substrates. Interestingly, aryl chlorides containing a formyl group could also be used, provided that the formyl group was temporarily converted into an α-amino alkoxide by using the lithium amide of <i>N</i>,<i>N</i>,<i>N</i>′-trimethylethylenediamine (LiTMDA). The presence of a hydroxyl group was also tolerated when it was deprotonated with <i>n</i>-BuLi prior to the addition of LiDBB.
An Efficient Algorithm for Sparse Quantum State Preparation (2021)

Generating quantum circuits that prepare specific states is an essential part of quantum compilation. Algorithms that solve this problem for general states generate circuits at grow exponentially in the number of qubits. However, in contrast to general states, many practically relevant states are sparse in the standard basis. In this paper we show how sparsity can be used for efficient state preparation. We present a polynomial-time algorithm that generates polynomial-size quantum circuits (linear in the number of nonzero coefficients times number of qubits) that prepare given states, making computer-aided design of sparse state preparation scalable.