gebhart/patrepeval huggingface dataset:
Coiled-Tubing Fracturing: An Operational Review of a 43-Stage Barnett Shale Stimulation (2010)

Abstract Traditional multi-stage high rate fracture treatments have been used in many shale and conventional formations. These treatments typically rely on composite bridge or frac plugs, run on wireline to provide zonal isolation. In a typical frac treatment, rates of up to 100 bpm are normally divided between four to six pre-perforated clusters per stage. Typical spacings between clusters are 50 to 100 ft. In theory, fluid would divide equally between each perforated cluster, however that is an unlikely scenario since stimulation treatments will follow the path of least resistance. To improve production results, targeted fracturing operations are gaining in popularity in many formations. Some targeted operations utilize abrasive perforating via coiled tubing (CT), followed by the fracture treatment down the annulus. The treatment flush is modified to include an underdisplaced dense slurry stage to act as the isolation mechanism. In vertical wells, proppant settles by gravity covering the recently treated interval. In horizontal wells however, a plug enhancement additive (PEA) can be used to achieve isolation, partially mitigating gravity effects. Moreover, instead of splitting flow between four to six clusters, most horizontal treatments target only one discreet cluster/zone at a time. Significant gains in fracture control are obtained with this method. Initial targeted operations were applied to 300 ft of frac spacing, thus reducing the number of stages per well when compared to the 50 to 100 ft cluster spacing on higher rate frac operations. This paper describes one targeted operation in a horizontal well where the spacing was reduced to 60 ft. In all, forty-three stages were successfully stimulated using enhanced sand plugs for zonal isolation.
Amygdalae morphometry in late‐life depression (2008)

In this LLD study, we have shown that, despite insignificant amygdalar volumetric findings, variations of amygdalar shape can be detected and localized. With further investigation, morphometric analysis of various brain structures may help elucidate the neurobiology associated with LLD and other mood disorders.
Short-Term Adverse Outcomes Associated With Hypoglycemia in Critically Ill Children (2019)

When a computerized algorithm, continuous glucose monitors and standardized glucose infusion rates were used to manage hyperglycemia in critically ill children with cardiovascular and/or respiratory failure, severe hypoglycemia (blood glucose < 40 mg/dL) was uncommon, but any hypoglycemia (blood glucose < 60 mg/dL) remained common and was associated with worse short-term outcomes.
Laser Microdissection of the Alveolar Duct Enables Single-Cell Genomic Analysis (2014)

Complex tissues such as the lung are composed of structural hierarchies such as alveoli, alveolar ducts, and lobules. Some structural units, such as the alveolar duct, appear to participate in tissue repair as well as the development of bronchioalveolar carcinoma. Here, we demonstrate an approach to conduct laser microdissection of the lung alveolar duct for single-cell PCR analysis. Our approach involved three steps. (1) The initial preparation used mechanical sectioning of the lung tissue with sufficient thickness to encompass the structure of interest. In the case of the alveolar duct, the precision-cut lung slices were 200 μm thick; the slices were processed using near-physiologic conditions to preserve the state of viable cells. (2) The lung slices were examined by transmission light microscopy to target the alveolar duct. The air-filled lung was sufficiently accessible by light microscopy that counterstains or fluorescent labels were unnecessary to identify the alveolar duct. (3) The enzymatic and microfluidic isolation of single cells allowed for the harvest of as few as several thousand cells for PCR analysis. Microfluidics based arrays were used to measure the expression of selected marker genes in individual cells to characterize different cell populations. Preliminary work suggests the unique value of this approach to understand the intra- and intercellular interactions within the regenerating alveolar duct.
ARCH++: Animation-Ready Clothed Human Reconstruction Revisited (2021)

We present ARCH++, an image-based method to reconstruct 3D avatars with arbitrary clothing styles. Our reconstructed avatars are animation-ready and highly realistic, in both the visible regions from input views and the unseen regions. While prior work shows great promise of reconstructing animatable clothed humans with various topologies, we observe that there exist fundamental limitations resulting in sub-optimal reconstruction quality. In this paper, we revisit the major steps of image-based avatar reconstruction and address the limitations with ARCH++. First, we introduce an end-to-end point based geometry encoder to better describe the semantics of the underlying 3D human body, in replacement of previous hand-crafted features. Second, in order to address the occupancy ambiguity caused by topological changes of clothed humans in the canonical pose, we propose a co-supervising framework with cross-space consistency to jointly estimate the occupancy in both the posed and canonical spaces. Last, we use image-to-image translation networks to further refine detailed geometry and texture on the reconstructed surface, which improves the fidelity and consistency across arbitrary viewpoints. In the experiments, we demonstrate improvements over the state of the art on both public benchmarks and user studies in reconstruction quality and realism.
On the Capacity of Generalized Ising Channels (2016)

Nearly tight lower and upper bounds on the capacity of generalized Ising channels are presented. For the case where feedback is allowed, a closed-form expression for the capacity is found for channel error probability p ∈ [0, p0], where p0 ≈ 0.398324. A near-capacity-achieving family of encoders is presented for the values p ∈ [0, p0]. Two lower bounds on that capacity for larger values of p are presented, one of which is tight on the interval [p0, 0.5].
Interstitial Pneumonia With Autoimmune Features: Value of Histopathology (2017)

- Using a methodological approach to identifying IPAF pathology, we demonstrate a significant increase in the number of patients meeting IPAF criteria because of focused pathologic review and highlight the prognostic value of the IPAF pathologic findings.
Piezoelectric Sensors: Self‐Powered Real‐Time Arterial Pulse Monitoring Using Ultrathin Epidermal Piezoelectric Sensors (Adv. Mater. 37/2017) (2017)

In article number 1702308, Keon Jae Lee and co-workers demonstrate a self-powered, flexible piezoelectric pressure sensor on an ultrathin substrate via an inorganic-based laser lift-off process for detecting various physiological signals in near-surface arteries. The radial pulse signals are wirelessly transmitted to a smart phone using a Bluetooth module, which realizes the possibility of a self-powered and real-time healthcare-monitoring system.
Infrared Multiphoton Dissociation Spectroscopic Analysis of Peptides and Oligosaccharides by Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with a Midinfrared Free-Electron Laser (2006)

The fragmentation of peptides and oligosaccharides in the gas phase was investigated by means of electrospray ionization Fourier transform ion cyclotron resonance (FTICR) mass spectrometry coupled with dissociation by a laser-cleavage infrared multiphoton dissociation (IRMPD) technique. In this technique, an IR free-electron laser is used as a tunable source of IR radiation to cause cleavage of the ionized samples introduced into the FTICR cell. The gas-phase IRMPD spectra of protonated peptides (substance P and angiotensin II) and two sodiated oligosaccharides (sialyl Lewis X and lacto-N-fucopentaose III) were obtained over the IR scan range of 5.7-9.5 microm. In the IRMPD spectra for the peptide, fragment ions are observed as y/b-type fragment ions in the range 5.7-7.5 microm, corresponding to cleavage of the backbone of the parent amino acid sequence, whereas the spectra of the oligosaccharides have major peaks in the range 8.4-9.5 microm, corresponding to photoproducts of the B/Y type.
Synthesis of 10, 11-Dihydroxydihydroquinidine N-oxide, a New Metabolite of Quinidine. Preparation and 1H-nmr Spectroscopy of the Metabolites of Quinine and Quinidine and Conformational Analysis via 2D COSY NMR Spectroscopy (1990)

The first synthesis of 10,11-dihydroxydihydroquinidine N-oxide [7b], a recently isolated metabolite of quinidine, was accomplished in three steps from 1b. The related congener 7a in the quinine series was also prepared, as well as two other analogues 3a and 4a. In addition, the previously reported human metabolites 2a, 5a, and 6a of quinine [1a] and those 2b, 3b, 4b, 5b, and 6b of quinidine [1b] were synthesized. The chemical shift and coupling constants for all of the metabolites of quinine and quinidine were assigned via 2D COSY 1H-nmr spectroscopy. Moreover, the conformations of these metabolites in solution were found to parallel those of the parent alkaloids, quinine [1a] and quinidine [1b], respectively.
Single‐Layer Centrifugation Reduces Equine Arteritis Virus Titre in the Semen of Shedding Stallions (2012)

Several countries have adopted strategies for preventing and/or controlling equine viral arteritis based on vaccination and restricting the breeding activities of carrier stallions. However, in some cases, carrier stallions are only identified after they have transmitted virus to a mare. Therefore, a mechanism for separating virus from spermatozoa in the semen of carrier stallions would facilitate control measures for preventing disease transmission. In this study, the use of several modifications of single-layer centrifugation (SLC, SLC with an inner tube and double SLC) through Androcoll-E, a species-specific colloid were evaluated for their ability to separate spermatozoa from virus in ejaculates from carrier stallions. The three types of SLC significantly reduced the virus titre in fresh semen at 0 h and in stored semen at 24 h (p < 0.001) but did not completely eliminate the virus. Sperm motility parameters such as total motility and progressive motility were significantly increased after colloid centrifugation, whereas curvilinear velocity and amplitude of lateral head deviation were decreased, and the remainder (straight line velocity, average path velocity, straightness, linearity, wobble and beat cross-frequency) were not significantly affected by the processing. Although virus titres were reduced in the SLC samples, significant levels of infectivity still remained, especially in stallions shedding large amounts of virus. It remains to be determined whether SLC-processed sperm samples from stallions shedding low virus titres retain sufficient equine arteritis virus to cause infection in mares through artificial insemination.
Cloning and disruption of the gene encoding an extracellular metalloprotease of Aspergillus fumigatus (1994)

Aspergillus fumigatus secretes a serine alkaline protease (ALP) and a metalloprotease (MEP) when the fungus is cultivated in the presence of collagen as sole nitrogen and carbon source. The gene encoding ALP was isolated and characterized previously. We report here the cloning and the sequencing of the gene encoding MEP. Genomic and cDNA clones were isolated from A. fumigatus libraries using synthetic oligonucleotides as probes. Stretches of the deduced amino acid sequence were found to be in agreement with the N-terminal amino acid sequence of MEP and with internal peptide sequences. The amino acid sequence of the enzyme contains a putative active-site sequence HEYTH homologous to the active site of other bacterial and eukaryotic zinc metalloproteases. Sequence analysis reveals that MEP has a pre-proregion consisting of 245 amino acid residues preceding the 388 amino acid residues of the mature region (molecular mass of 42 kDa). An alp mep mutant, deficient in proteolytic activity at neutral pH in vitro, was constructed and tested for pathogenicity in a murine model. No difference in pathogenicity was observed between the wild-type strain and the alp mep double mutant, suggesting that ALP and MEP are not essential for the invasion of the lung tissues by A. fumigatus.
Herpes simplex virus type I (HSV-1) replicates in mature dendritic cells but can only be transferred in a cell–cell contact-dependent manner (2011)

HSV-1 is a very successful representative of the α-herpesvirus family, and ∼ 90% of the population is seropositive for this particular virus. Although the pathogen usually causes the well-known mild lesions on the lips, also, severe infections of the eye or the brain can be observed in rare cases. It is well known, that this virus can efficiently infect the most potent APCs, i.e., the DCs, in their immature and mature state. Although the infection of the iDC has been shown to be productive, infection of mMDDCs is believed to be abortive in the early phase of the viral replication cycle. In line with these findings, no virus particles can be detected in the supernatant of HSV-1-infected mMDDC. In this study, however, we show for the first time that this pathogen completes its replication cycle in mMDDCs. We detected the presence of viral gene transcripts of all three phases of the replication cycle, as well as of late viral proteins, and even the generation of small amounts of progeny virus. Although we could confirm the findings that these particles are not released into the supernatant, surprisingly, the newly generated viral particles can be passed on to Vero cells, as well as to primary keratinocytes in a cell-cell contact-dependent manner. Finally, we provide evidence that the viral gE is involved in the transfer of infectious virus from mMDDCs to other permissive cells.
Influence of Some Design Variables on the Thermal Behavior of a Lithium‐Ion Cell (1999)

A mathematical model that includes an anode (carbon) decomposition reaction has been used to predict the temperature of a lithium‐ion cell during medium‐ and high‐rate discharge conditions. This work describes how various design parameters and the activation energy for the decomposition reaction of the anode (carbon) affect the predicted temperature of a cell. The predicted results show that the particle size in the negative electrode (assumed here to be petroleum coke) is an important parameter for predicting the temperature of the cell. © 1999 The Electrochemical Society. All rights reserved.
Improving SVT Discrimination in Single‐Chamber ICDs: A New Electrogram Morphology‐Based Algorithm (2006)

Results from this prospective study of the Wavelet electrogram morphology discrimination algorithm operating as the sole discriminator in the ON mode demonstrate that inappropriate therapy for supraventricular tachycardia in a single-chamber ICD can be dramatically reduced compared to rate detection alone.
Synthesis and characterization of phosphorescent three-coordinate Cu(i)–NHC complexes (2010)

Cationic and neutral monomeric three-coordinate phosphorescent Cu(I) complexes were synthesized and characterized by XRD analysis, electrochemistry and photophysical studies in different environments. DFT calculations have aided the assignment of the electronic structure and excited state behavior of these complexes.
Feed Composition and Isolate of Histomonas meleagridis Alter Horizontal Transmission of Histomonosis in Turkeys. Proof of Concept (2022)

Outbreaks of histomonosis in turkeys are typically initiated by the ingestion of contaminated embryonated eggs of Heterakis gallinarum , potentially present in earthworms and mechanical vectors. Once an outbreak is started, infected turkeys can transmit the disease by horizontal transmission. Factors influencing horizontal transmission of histomonosis are poorly understood. Replication of horizontal transmission in experimental conditions has not been consistent, presenting an obstacle in searching for alternatives to prevent or treat the disease. Two pilot experiments and three validation experiments were conducted in the present study. In pilot experiment 1, one isolate of Histomonas meleagridis (named Buford) was used. Turkeys were fed a low-nutrient density diet corn-soy based (LOW-CS) and raised in floor pens. In pilot experiment 2, another isolate of H. meleagridis was used (named PHL). Turkeys were fed a low-nutrient density diet with the addition of wheat middlings (LOW-WM) and raised in floor pens. In experiment 3, conducted on floor pens, both isolates and diets were used in different groups. In experiment 4, turkeys were raised on battery cages and only the PHL isolate was used. Both diets (LOW-WM and LOW-CS) were used, in addition to a diet surpassing the nutritional needs of young poults (turkey starter, TS). In experiment 5, conducted in battery cages, only the PHL isolate was used, and the LOW-WM and TS diets were in different groups. The horizontal transmission was achieved only with the PHL isolate from all experiments. The transmission rate varied among experimental diets, with the TS diet having the lowest transmission rate in experiments 4 and 5. Variation was observed between experiments and within experimental groups.
Abstract 1524: Peripheral blood mononuclear cells engineered via microfluidic Cell Squeeze® technology to generate APCs that drive mutant-KRas-specific CD8+ T cell responses (2021)

Abstract KRAS mutations are shared across multiple cancer types and are most commonly found in cancers of the lung, pancreas, and colon. While recently developed drugs blocking signaling driven by KRAS G12C mutations have shown promise in the clinic, there is a great need for therapies targeting the more common G12V and G12D mutations. We utilize our microfluidic Cell Squeeze® technology to deliver antigens directly into the cytosol of peripheral blood mononuclear cells (PBMCs) for the generation of cancer antigen-targeted cellular vaccines. This method bypasses the need for cross-presentation and directly enables efficient antigen presentation on MHC-I in multiple cell types. Murine and human in vitro studies have demonstrated that this allows SQZ PBMCs to drive CD8+ T cell activation. Here, we demonstrate the delivery of various antigens, including KRas-derived peptides containing the most common mutations (G12D and G12V) to PBMC cell subsets. In addition, we find that human PBMCs squeezed with either KRasG12V or KRasG12D peptides can specifically stimulate KRasG12V- and KRasG12D- reactive CD8+ T cell responders. When KRasG12V and KRasG12D peptides are co-delivered via microfluidic squeezing, the human PBMCs enable activation of CD8+ T cells of both specificities. This work with KRasmutant-presenting human PBMCs lays a strong foundation for developing a potentially potent cell therapy to treat KRASmutant associated cancers. Citation Format: Defne Yarar, Carolyne Smith, Amritha Ramakrishnan, Scott Loughhead, Armon Sharei, Katherine Seidl, Howard Bernstein. Peripheral blood mononuclear cells engineered via microfluidic Cell Squeeze® technology to generate APCs that drive mutant-KRas-specific CD8+ T cell responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1524.
$H^2 $-Functions and Infinite-Dimensional Realization Theory (1975)

In this paper the realization question for infinite-dimensional linear systems is examined for both bounded and unbounded operators. In addition to obtaining realizability criteria covering the basic cases, we discuss the relationship between canonical realizations of the same system. What one finds is that the set of transfer functions which are realizable by triples $(A,b,c)$ with A bounded is related in a close way to the space of complex functions analytic and square integrable on the disk $| {s < 1} |$, and that the set of transfer functions which are realizable by triples $(A,b,c)$ with A unbounded but generating a strongly continuous semigroup is related in a close way to functions analytic and square integrable on a half-plane. This relation makes possible a deeper study between the transfer function and the models which realize it. Some examples illustrate the results and their applications.
Intramolecular Reactivity of trans [4+4] Photodimers of 2-Pyridones (2007)

Photodimers of 2-pyridones are cycloocta-1,5-dienes with two lactam bridges. These, and related structures, undergo halogenation to give rearranged products in which an amide nitrogen has intercepted an initial halonium ion. For the trans isomer, a transient four-membered azetidinium ion reacts via dealkylation, giving a dihalide-diamide product in high yield. This readily available intermediate reacts with nucleophiles in a process that begins with intramolecular amide N-alkylation, reforming the azetidinium intermediate. Reaction of this intermediate with the nucleophile can take two different paths, depending on the reversibility of the nucleophilic attack, with reversible nucleophiles giving N-dealkyl­ation and irreversible nucleophiles reacting with the carbonyl group.
A Potent and Selective AMPK Activator That Inhibits de Novo Lipogenesis (2010)

AMP-activated protein kinase (AMPK) is a heterotrimeric kinase that regulates cellular energy metabolism by affecting energy-consuming pathways such as de novo lipid biosynthesis and glucose production as well as energy-producing pathways such as lipid oxidation and glucose uptake. Accordingly, compounds that activate AMPK represent potential drug candidates for the treatment of hyperlipidemia and type 2 diabetes. Screening of a proprietary library of AMP mimetics identified the phosphonic acid 2 that bears little structural resemblance to AMP but is capable of activating AMPK with high potency (EC50 = 6 nM vs AMP EC50 = 6 μM) and specificity. Phosphonate prodrugs of 2 inhibited de novo lipogenesis in cellular and animal models of hyperlipidemia.
Optimization of enzyme immobilization on magnetic microparticles using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) as a crosslinking agent (2015)

Enzyme immobilization is a versatile tool in biotransformation processes to enhance enzyme activity and to secure an easy separation of catalysts and products and the reusability of enzymes.
Canine Intestinal Spirochetes Consist of Serpulina pilosicoli and a Newly Identified Group Provisionally Designated “ Serpulina canis ” sp. nov (1998)

The spirochetes inhabiting the large intestines of humans and animals consist of a diverse group of related organisms. Intestinal spirochetosis caused by Serpulina pilosicoli is a newly recognized enteric disease of human beings and animals with potential public health significance. The purpose of this study was to determine the species identity of canine intestinal spirochetes by comparing 30 isolates obtained from dogs in Australia (n = 25) and the United States (n = 5) with reference strains representing Serpulina species and Brachyspira aalborgi, by phenotypic and genetically based typing methods. All of the canine isolates were indole negative and produced a weak beta-hemolysis when cultured anaerobically on agar medium containing blood. Four isolates were identified as S. pilosicoli by 16S rRNA-specific PCR assays, rRNA gene restriction fragment length polymorphism or ribotyping, and multilocus enzyme electrophoresis. The remaining 26 isolates formed a cluster related to porcine Serpulina innocens as determined by multilocus enzyme electrophoresis but had a unique ribotype pattern. The data suggested the existence of a novel Serpulina species, provisionally designated "Serpulina canis," colonizing the intestines of dogs.