gebhart/patrepeval huggingface dataset:
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness (2011)

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger- and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80,000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36,000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100,000-500,000 species), suggesting a degree of protistan endemism.
MALDI-TOF MS for Environmental Analysis, Microbiome Research and as a Tool for Biological Resource Centres (2016)

Recent years have seen a phenomenal increase in the use of MALDI-TOF mass spectrometry (MALDI-TOF MS) in microbiology laboratories.The introduction of this technology to microbiology has been a major success and MALDI-TOF MS is now used for routine diagnostic or diagnostic-like purposes in clinic, veterinary, pharma and food microbiology laboratories.It has also evolved into a powerful tool for the analysis of organisms in the environment and for research into microbial communities.The throughput capabilities, accuracy and low running costs of a MALDI-TOF MS system enable analyses at a scale which was not possible until recently.In this timely and up-to-date book, experts in the field provide an overview of the application of MALDI-TOF MS in key areas of microbiology and discuss the impact this modern technology is having on laboratory practice and patient outcome.Several chapters cover applications in clinical and veterinary diagnostic laboratories, food microbiology, environmental microbiology and strain collections.Further chapters discuss the utilization of MALDI-TOF MS for the analysis of challenging microbial groups such as yeast and anaerobic bacteria.In addition, new applications such as microbial typing, DNA analysis and the detection of antibiotic resistance are also covered.The final chapter provides a valuable overview of potential future trends and developments in MALDI-TOF MS and assesses the impact of the technology in microbiology.This authoritative volume will be indispensable for all microbiology laboratories.Introduction.A Personal Vision of the MALDI-TOF-MS Journey from Obscurity to Frontline Diagnostics (Haroun N. Shah) Chapter 1. Matrix Assisted Laser Desorption Ionization
Bioinformatic Networks: Molecular Reticles for Pinpointing Pharmacological Target Selection (2008)

Bridging centrality was developed as a novel metric to capitalize on rich biological networks and enable selection of therapeutically efficient, druggable candidates. Through incorporation of local and global network properties, targetable nodes are identified that harbor latent capacity to intercept informational flow without compromising systemic functionality. Translational implementation holds potential for increased therapeutic specificity and offers opportunities to add value to drug discovery and development through facilitation of individualized treatment.
Microphase Separation of Hybrid Dendron−Linear Diblock Copolymers into Ordered Structures (2002)

Hybrid copolymers with dendritic−linear blocks are shown to exhibit many of the classic microphase-separated structures of linear−linear block copolymers. Transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and small-angle neutron scattering (SANS) were used to evaluate the morphology of a sixth generation (G6) poly(benzyl ether) dendron covalently bonded to linear polystyrene (PS) at the dendron focal point. Increasing the fraction of the linear block, φPS, through an increase in the molecular weight of the PS block revealed morphologies evolving from disordered to ordered lamellar to hexagonally close-packed dendron cylinders. Significantly, the observed morphologies are distinct from those expected for analogous linear−linear blocks at equivalent volume fraction, although the direction of progression follows expectation. Quantitative analysis suggests substantial molecular deformation or shape change in the dendritic phase. The possible role of conformational entropy in determining the overall free energy is suggested to be important for this class of block copolymer.
Nylon-3 Polymers with Selective Antifungal Activity (2013)

Host-defense peptides inhibit bacterial growth but show little toxicity toward mammalian cells. A variety of synthetic polymers have been reported to mimic this antibacterial selectivity; however, achieving comparable selectivity for fungi is more difficult because these pathogens are eukaryotes. Here we report nylon-3 polymers based on a novel subunit that display potent antifungal activity (MIC = 3.1 μg/mL for Candida albicans ) and favorable selectivity (IC10 > 400 μg/mL for 3T3 fibroblast toxicity; HC10 > 400 μg/mL for hemolysis).
Comparison of Effects of Diet on Mammary Cancer: Efficacy of Various Preventive Agents and Metabolomic Changes of Different Diets and Agents (2018)

To determine the effects of diet, rats were placed on a standard diet (4% fat) or on a modified Western (high-fat diet, HFD) diet (21% fat) at 43 days of age (DOA) and administered methylnitrosourea (MNU) at 50 DOA. Rats were administered effective (tamoxifen, vorozole, and Targretin) or ineffective (metformin and Lipitor) chemopreventive agents either by daily gavage or in the diet beginning at 57 DOA and continuing until sacrifice (190 DOA). Latency period of the tumors was determined by palpation, and multiplicity and cancer weights per rat were determined at final sacrifice. Rats on the HFD versus standard diet had: (i) a 6% increase in final body weights; (ii) significant decreases in tumor latency; and (iii) significant increases in final tumor multiplicity and average tumor weight. Tamoxifen, vorozole, and Targretin were highly effective preventive agents, whereas Lipitor and metformin were ineffective in rats on either diet. Serum was collected at 78 DOA and at sacrifice (190 DOA), and metabolomics were determined to identify the metabolite changes due to diets and effective agents. Rats given the HFD had increased levels of saturated free fatty acids (including myristate) and decreased levels of 2-aminooctanoate. Furthermore, rats on the HFD diet had increased levels of 2-aminobutyrate and decreases in glycine markers previously identified as indicators of prediabetes. Targretin increased long-chain glycophospholipids (e.g., oleyl-linoleoyl-glycerophosphocholine) and decreased primary bile acids (e.g., taurocholate). Tamoxifen increased palmitoyl-linoleoyl-glycophosphocholine and decreased stearoyl-arachidonyl glycophosphocholine. Finally, increased levels of methylated nucleotides (5-methylcytidine) and decreased levels of urea cycle metabolites (N-acetylcitrulline) were associated with the presence of mammary cancers.
Synthesis of a novel hexaarylbiimidazole with ether groups and characterization of its photoinitiation properties for acrylate derivatives (2006)

Abstract A novel photoinitiator 2,2′‐bis‐(2‐chlorophenyl)‐4,4′,5,5′‐tetra‐[3‐(2‐hydroxylmethyl‐2‐triethylene glycol monoethylene ether‐ethane‐1‐oxy)‐phenyl]‐1,2′‐biimidazole (BCTE‐HABI) was synthesized from 3,3′‐dimethoxy benzoin. Ultraviolet spectra, fluorescence spectra, ESR, photodilatometer, and photo‐DSC measurements indicate that its photoinitiating activity for acrylate derivatives is better than 2,2′‐bis‐(2‐chlorophenyl)‐4,4′,5,5′‐tetraphenyl‐1,2′‐biimidazole ( o ‐Cl‐HABI), which is one of the most widely studied and used derivatives of HABI. POLYM. ENG. SCI., 46:474–479, 2006. © 2006 Society of Plastics Engineers.
Abstract A044: Immunological effects of a novel RNA-based adjuvant in liver cancer patients (2016)

Abstract Evaluation of detailed biological effects of adjuvants on immune cells has been assessed in a limited number of studies performed only on samples derived from healthy individuals. No data are available on samples derived from cancer patients who may have a severe immune impairment. A novel RNA-based adjuvant (RNAdjuvant® developed by CureVac) is made of a synthetic single stranded RNA molecule combined with a polymeric carrier. It is known to interact with toll-like receptors (TLRs) 7. The effects of RNAdjuvant® on PBMCs of liver cancer patients was assessed in an ex vivo setting, using a multiparametric approach to analyze network dynamics of early human immune responses. PBMCs were obtained from 8 healthy volunteers and 17 HCC patients enrolled in the present study. After treatment in culture, the effects of RNAdjuvant® were assessed by evaluation of CD80, CD86 and HLA-DR expression, pattern of cytokine production as well as gene expression profile. Moreover, the downstream effect on CD4+ T cell phenotyping was evaluated. The TLR4 ligand LPS was used as comparison. Treatment with RNAdjuvant® showed comparable effects on PBMCs of both HCC and healthy subjects, as shown by all the evaluated parameters. CD80, CD86 and HLA-DR expression was found upregulated in circulating dendritic cells, which promoted a CD4+ T cell differentiation towards an effector phenotype. A mixed Th1/Th2 cytokine pattern was induced in PBMCs, although a more predominant production of TNFα and IFNγ was observed in HCC patients vs. healthy controls. The cytokine profile was further confirmed by gene transcriptional analysis, which showed up-regulation of several genes involved in innate and adaptive immune-related pathways. Citation Format: Luisa Circelli, Annacarmen Petrizzo, Maria Tagliamonte, Regina Heidenreich, Maria Lina Tornesello, Franco M. Buonaguro, Luigi Buonaguro. Immunological effects of a novel RNA-based adjuvant in liver cancer patients [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A044.
An Actuarial Model of Autonomous Vehicles (2017)

The technology of autonomous vehicles is growing fast in current time. On one hand, the popularization of autonomous vehicles is expected to greatly reduce the occurrence of traffic accidents, meanwhile lowers the income of premium for insurance companies; on the other hand, the decrease of traffic accidents also reduces the amount of claim for these companies.
Optimized In-Band Full-Duplex MIMO Relay Under Single-Stream Transmission (2015)

This paper presents a coherent scheme to optimize an in-band full-duplex multiple-input-multiple-output (MIMO) relay via beamforming and transmit power allocation in a two-hop single-input-single-output (SISO) link under full channel knowledge and perfect hardware assumptions. First, we derive in closed form the optimal pair of transmit power and receive filter for a fixed transmit filter by unifying the minimum-mean-square-error (MMSE) filtering with the SISO-equivalent power allocation, as an iterative approach is not guaranteed to converge to global optimum. Second, we propose a heuristic algorithm to approximate the optimal transmit filter for a fixed receive filter. Furthermore, we study the well-known null-space projection constraint and derive a singular value decomposition (SVD)-based solution for the arbitrary-rank self-interference channel by generalizing the optimal solution under the assumption of rank-1 self-interference channel. Finally, we combine these solutions into a partially iterative algorithm in order to address the global optimization as our observations justify that some of the aforementioned schemes converge to the optimal solution under certain criteria. The numerical analysis of the proposed iterative algorithm demonstrates close-to-optimal performance relative to the theoretical upper bound of the end-to-end link in terms of maximum achievable throughput.
Geometry-Dependent Spectroscopic Contrast in Deep Tissues (2019)

Nano-structures of biological systems can produce diverse spectroscopic effects through interactions with broadband light. Although structured coloration at the surface has been extensively studied, natural spectroscopic contrasts in deep tissues are poorly understood, which may carry valuable information for evaluating the anatomy and function of biological systems. Here we investigated the spectroscopic characteristics of an important geometry in deep tissues at the nanometer scale: packed nano-cylinders, in the near-infrared window, numerically predicted and experimentally proved that transversely oriented and regularly arranged nano-cylinders could selectively backscatter light of the long wavelengths. Notably, we found that the spectroscopic contrast of nanoscale fibrous structures was sensitive to the pressure load, possibly owing to the changes in the orientation, the degree of alignment, and the spacing. To explore the underlying physical basis, we further developed an analytical model based on the radial distribution function in terms of their radius, refractive index, and spatial distribution.
ChemInform Abstract: NUCLEOSIDES. XXXIV. RIBOSYLATIONS OF 5,6‐DIHYDRO‐6‐OXOLUMAZINE AND ITS 1,3‐DIMETHYL DERIVATIVE (1981)

Abstract Im Rahmen eingehender Studien über das Verhalten des Lumazin‐Systems bei Ribosidierungs‐Reaktionen werden die aus den Titelverbindungen (Ia) bzw. (Ib) zugänglichen Silyl‐Derivate (II) bzw. (VI) der Ribosidierung mit der geschützten β‐D‐Ribofuranose (III) in Gegenwart von BF3°C Et2O als Katalysator unterworfen.
Functional Materials for 3D Manufacturing using Carbon's CLIP Technology (2016)

We demonstrate a series of materials compatible on Carbon's light-based CLIP technology that exhibit a range of useful properties for final manufactured parts in a variety of applications.
Collision-induced dissociation and density functional study of the structures and energies of cyclic C2nN5− clusters (2000)

In this paper, we report mass spectrometry studies on C2nN5− cluster ions by collision-induced dissociation (CID). The mass-selected cluster ions were dissociated by collision with a crossed nitrogen beam and the fragment ions were mass analyzed in a secondary mass spectrometer. Characterization of the species as cyano-substituted, planar five-membered rings is supported by density functional theory (DFT) calculations. Based on the analysis of the experimental and computational results, cluster structures, energies, and stabilities are discussed.
Crystal phase and growth orientation dependence of GaAs nanowires on NixGay seeds via vapor-solid-solid mechanism (2011)

One of the challenges to utilize high performance III-V compound semiconductor nanowires (NWs) for large-scale technological applications is to control the crystal phase and growth orientation for homogenous nanowire properties. Here, we report the dependence of crystal structure and growth orientation of GaAs NWs on NixGay seeds via vapor-solid-solid mechanism. The crystal structure of catalytic seeds is found to direct the crystal phase of NWs with cubic NiGa seeds yielding zincblende GaAs NWs while hexagonal Ni2Ga3 seeds producing wurtzite GaAs NWs. Furthermore, the seed/nanowire interface plane relationship would dictate the epitaxial growth orientation of NWs, which is independent of the NW diameters and growth conditions. All these suggest the importance of well-controlled phase and orientation of catalysts for the synthesis of homogenous nanowires.
Asymmetric Synthesis and Application of Homologous Pyrroline‐2‐alkylboronic Acids: Identification of the B–N Distance for Eliciting Bifunctional Catalysis of an Asymmetric Aldol Reaction. (2013)

Abstract Homoboroproline has been shown to be an efficient bifunctional catalyst for the aldol reaction of acetone with p ‐nitrobenzaldehyde by using in situ Lewis acid tuning of the boronic acid esterification with a diol. Herein, asymmetric syntheses of homologues of this catalyst are developed to compare their catalytic capability and chemical properties with homoboroproline, and to probe the effect that chain‐length separation of the amino and boronate groups has on the intramolecular B–N coordination, as well as other cooperative interactions, to explain their widely differing catalytic properties.
Trench multiplication process by a sacrificial SiGe epitaxial Layer (2014)

Trench etching is an important process step for many semiconductor applications. Memory implementations, power devices and embedded capacitors benefit from lateral shrinkage of trench dimensions. But for physical reasons the depth of a trench that can be achieved for a given diameter is limited. We describe here a process with a sacrificial Silicon-Germanium (SiGe) layer on the sidewall of a trench, that multiplies the number of trenches in a unit cell by five with a correspondent improvement of the aspect ratio, avoiding the difficulties of reactive ion etching.
Optical characterization of anisotropic plastics (1997)

Plastics have many commercial applications including photographic film and display technology. They often exhibit biaxial anisotropy due to extrusion and stretching during preparation. The characterization of coatings on plastic will improve when the plastic optical properties are understood. Plastic processing can also be monitored through its optical properties.
Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana (2022)

A novel Gram-stain-positive, aerobic bacterial strain, designated AK-R2A1-2<sup> T</sup>, was isolated from the surface-sterilized needle leaves of an Abies koreana tree. Strain AK-R2A1-2<sup> T</sup> had 97.3% and 96.7% 16S rRNA gene sequence similarities with Subtercola boreus K300<sup>T</sup> and Subtercola lobariae 9583b<sup>T</sup>, respectively, but formed a distinct phyletic lineage from these two strains. Growth of strain AK-R2A1-2<sup> T</sup> was observed at 4-25 °C at pH 5.0-8.0. Strain AK-R2A1-2<sup> T</sup> contained menaquinone 9 (MK-9) and menaquinone 10 (MK-10) as the predominant respiratory quinones. The major cellular fatty acids were anteiso-C<sub>15:0</sub> and summed feature 8 (C<sub>18:1</sub>ω7c or/and C<sub>18:1</sub>ω6c), and the polar lipids included diphosphatidylglycerol (DPG) and three unknown aminolipids, AKL2, AKL3, and AKL4. The complete genome of strain AK-R2A1-2<sup> T</sup> was sequenced to understand the genetic basis of its survival at low temperatures. Multiple copies of cold-associated genes involved in cold-active chaperon, stress response, and DNA repair supported survival of the strain at low temperatures. Strain AK-R2A1-2<sup> T</sup> was also able to significantly improve rice seedling growth under low temperatures. Thus, this strain represents a novel species of the genus Subtercola, and the proposed name is Subtercola endophyticus sp. nov. The type strain is AK-R2A1-2<sup> T</sup> (= KCTC 49721<sup> T</sup> = GDMCC 1.2921<sup> T</sup>).
Bidirectional ROF Transmission and Signal Remodulation Using Separate Optical Clock Distribution to Mitigate Signal Distortions (2009)

We demonstrate a bidirectional ROF system using a separate optical-clock distribution to mitigate signal-fading and code time-shifting. Error-free signal remodulation using downlink DPSK and uplink OOK was achieved in a 20-km reach ROF system.
Mean serum-level of common organic pollutants is predictive of behavioral severity in children with autism spectrum disorders (2016)

Autism spectrum disorders (ASD), and their pathogenesis, are growing public health concerns. This study evaluated common organic pollutant serum-concentrations in children, as it related to behavioral severity determined by rating scales and the Autism Diagnostic Observation Schedule (ADOS). Thirty children, ages 2-9, with ASD and thirty controls matched by age, sex, and socioeconomic status were evaluated using direct blood serum sampling and ADOS. Pooling concentrations of all studied pollutants into a single variable yielded cohort-specific neurobehavioral relationships. Pooled serum-concentration correlated significantly with increasing behavioral severity on the ADOS in the ASD cohort (p = 0.011, r = 0.54), but not controls (p = 0.60, r = 0.11). Logistic regression significantly correlated mean pollutant serum-concentration with the probability of diagnosis of behaviorally severe autism, defined as ADOS >14, across all participants (odds ratio = 3.43 [95% confidence: 1.14-10.4], p = 0.0287). No specific analyte correlated with ADOS in either cohort. The ASD cohort displayed greater quantitative variance of analyte concentrations than controls (p = 0.006), suggesting a wide range of detoxification functioning in the ASD cohort. This study supports the hypothesis that environmental exposure to organic pollutants may play a significant role in the behavioral presentation of autism.
The tactile dimension: a method for physicalizing touch behaviors (2023)

Traces of touch provide valuable insight into how we interact with the physical world. Measuring touch behavior, however, is expensive and imprecise. Utilizing a fluorescent UV tracer powder, we developed a low-cost analog method to capture persistent, high-contrast touch records on arbitrary objects. We describe our process for selecting a tracer, methods for capturing, enhancing, and aggregating traces, and approaches to examining qualitative aspects of the user experience. Three user studies demonstrate key features of this method. First, we show that it provides clear and durable traces on objects representative of scientific visualization, physicalization, and product design. Second, we demonstrate how this method could be used to study touch perception, by measuring how task and narrative framing elicit different touch behaviors on the same object. Third, we demonstrate how this method can be used to evaluate data physicalizations by observing how participants touch two different physicalizations of COVID-19 time-series data.
Decomposing Workload Bursts for Efficient Storage Resource Management (2010)

The growing popularity of hosted storage services and shared storage infrastructure in data centers is driving the recent interest in resource management and QoS in storage systems. The bursty nature of storage workloads raises significant performance and provisioning challenges, leading to increased resource requirements, management costs, and energy consumption. We present a novel workload shaping framework to handle bursty workloads, where the arrival stream is dynamically decomposed to isolate its bursts, and then rescheduled to exploit available slack. We show how decomposition reduces the server capacity requirements and power consumption significantly, while affecting QoS guarantees minimally. We present an optimal decomposition algorithm RTT and a recombination algorithm Miser, and show the benefits of the approach by evaluating the performance of several storage workloads using both simulation and Linux implementation.