gebhart/patrepeval huggingface dataset:
MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans (2016)

Serum miRNA levels show a link between deployment to locations with open burn pits and environmental exposures that can take place during deployment.
Ratios of Multijet Cross Sections inpp¯Collisions at√s=1.8TeV (2001)

We report on a study of the ratio of inclusive three-jet to inclusive two-jet production cross sections as a function of total transverse energy in p&pmacr; collisions at a center-of-mass energy sqrt[s] = 1.8 TeV, using data collected with the D0 detector during the 1992-1993 run of the Fermilab Tevatron Collider. The measurements are used to deduce preferred renormalization scales in perturbative O(alpha(3)(s)) QCD calculations in modeling soft-jet emission.
Do developmental problems perceived by parents of very-low-birth weight infants during the first year of life correlate with objective criteria at 2 years of age? (2013)

Aims: In a previous study we discovered that more than 50% of parents of very-low-birth weight (VLBW) infants describe a slower development than their peers during the first year of life. This rate increased to more than 70% with declining gestational age. We compared parental concern to development during the second year of life.
Foam Consolidation and Drainage (2012)

A theoretical model of foam as a consolidating continuum is proposed. The general model is applied to foam in a gravity settler. It is predicted that liquid drainage from foam in a gravity settler begins with a slow drainage stage. Next, a stage with faster drainage occurs where the drainage rate doubles compared to the initial stage. The experiments conducted within the framework of this work confirmed the theoretical predictions and allowed measurements of foam characteristics. Foams of three different concentrations of Pantene Pro-V Classic Care Solutions shampoo were studied, as well as the addition of polyethylene oxide (PEO) in one case. The shampoo's main foaming components are sodium lauryl sulfate and sodium laureth sulfate. It is shown to what extent foam drainage is slowed down by using higher shampoo concentrations and how it is further decreased by adding polymer (PEO).
OBSERVATIONS FROM BOREHOLE DILUTION LOGGING EXPERIMENTS IN FRACTURED CRYSTALLINE ROCK UNDER VARIABLE HYDRAULIC CONDITIONS (2014)

Identifying hydraulically active fractures in low permeability, crystalline-bedrock aquifers requires a variety of geophysical and hydrogeophysical borehole tools and approaches. One such approach is Single Borehole Dilution Tests (SBDT), which in some low flow cases have been shown to provide greater resolution of borehole flow than other logging procedures, such as vertical differential Heat Pulse Flowmeter (HPFM) logging. Because the tools used in SBDT collect continuous profiles of water quality or dye changes, they can identify horizontal flow zones and vertical flow. We used SBDT with a food grade blue dye as a tracer and dual photometer-nephelometer measurements to identify low flow zones. SBDT were conducted at seven wells with open boreholes (exceeding 300 ft). At most of the wells HPFM logs were also collected. The seven wells are set in low-permeability, fractured granite and gneiss rocks underlying a former tetrachloroeythylene (PCE) source area at the Savage Municipal Well Superfund site in Milford, NH. Time series SBDT logs were collected at each of the seven wells under three distinct hydraulic conditions: (1) ambient conditions prior to a pump test at an adjacent well, (2) mid test, after 2-3 days of the start of the pump test, and (3) at the end of the test, after 8-9 days of the pump test. None of the SBDT were conducted under pumping conditions in the logged well. For each condition, wells were initially passively spiked with blue dye once and subsequent time series measurements were made. Measurement accuracy and precision of the photometer tool is important in SBDT when attempting to detect low rates of borehole flow. Tests indicate that under ambient conditions, none of the wells had detectable flow as measured with HPFM logging. With SBDT, 4 of the 7 showed the presence of some very low flow. None of 5 (2 of the 7 wells initially logged with HPFM under ambient conditions were not re-logged) wells logged with the HPFM during the pump test had detectable flow. However, 3 of the 5 wells showed the patterns of very low flow with SBDT during the pump test including pumping induced changes of inflow and outflow patterns at one well.
Receivers for advanced optical modulation formats (2004)

We discuss advanced direct-detection receiver structures for a variety of optical amplitude- and phase-coded modulation formats, and point at format-specific design trade-offs.
Using full waveform inversion with limited-offset seismic data to improve presalt imaging in the Kwanza basin (2023)

Summary In deep-water Kwanza basin, offshore Angola, the pre-salt hydrocarbon potential remains under explored. This is, in part, due to the challenges associated with seismic exploration in this environment. The majority of seismic data in the area have limited offset and azimuth coverage, and reliable pre-salt imaging is highly dependent on having an accurate velocity model, especially in the presence of strong contrasts associated with carbonate and salt formations. Heritage seismic in the area often suffers from distortion and poor focusing of pre-salt targets, resulting in interpretation uncertainty. In this case study, we demonstrate how the application of contemporary data-processing and imaging workflows to heritage data from the area can significantly improve the reliability of pre-salt interpretation. Key to these improvements are the latest developments in full-waveform inversion which include multidimensional objective functions and automated decision making. These techniques allow us to overcome some of the challenges associated with the overburden geology and acquisition geometry, using both early arrivals and reflections to simultaneously update all geological units, even in the presence of strong contrasts.
Low level CpG island promoter methylation predicts a poor outcome in adult T-cell acute lymphoblastic leukemia (2019)

Cancer cells undergo massive alterations in their DNA methylation patterns which result in aberrant gene expression and malignant phenotypes. Abnormal DNA methylation is a prognostic marker in several malignancies, but its potential prognostic significance in adult T-cell acute lymphoblastic leukemia (T-ALL) is poorly defined. Here, we performed methylated DNA immunoprecipitation to obtain a comprehensive genome-wide analysis of promoter methylation in adult T-ALL (n=24) compared to normal thymi (n=3). We identified a CpG hypermethylator phenotype that distinguishes two T-ALL subgroups and further validated it in an independent series of 17 T-lymphoblastic lymphoma. Next, we identified a methylation classifier based on nine promoters which accurately predict the methylation phenotype. This classifier was applied to an independent series of 168 primary adult T-ALL treated accordingly to the GRAALL03/05 trial using methylation-specific multiplex ligation-dependent probe amplification. Importantly hypomethylation correlated with specific oncogenic subtypes of T-ALL and identified patients associated with a poor clinical outcome. This methylation-specific multiplex ligation-dependent probe amplification based methylation profiling could be useful for therapeutic stratification of adult T-ALL in routine practice. The GRAALL-2003 and -2005 studies were registered at http://www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively.
Regression of Deeply Infiltrating Giant Condyloma (Buschke-Löwenstein Tumor) Following Long-term Intralesional Interferon Alfa Therapy (2000)

In 1995, a 40-year-old heterosexual man developed a perianal tumor that rapidly increased in size. Following a clinical and histologic diagnosis of a large condyloma acuminatum (CA), the tumor was partially resected in a primary care hospital. Subsequently, recurrent perianal fistulae and abscesses required several surgical interventions, and the patient underwent a transverse colostomy to allow subsequent complete resection of the condyloma. At the patient’s first visit in our clinic in 1996, physical examination demonstrated a smooth, exophytic, cauliflowerlike perianal verrucous tumor extending toward the perineum, scrotum, and buttocks (Figure 1, left). A magnetic resonance imaging scan revealed that the tumor infiltrated deeply into the right side of the pelvis, including the ischiorectal fossa, internal obturator muscle, anal sphincter, perineum, and penile root (Figure2, top). Histologic reevaluation of a previously obtained biopsy specimen showed a large papillomatous tumor infiltrating deeply into the underlying tissues, without penetration of the basement membrane (Figure 3, top). The epithelium was acanthotic with blunt rete ridges, well stratified without apparent cellular atypia, and contained few mitoses and koilocytes (Figure 3, bottom). There was no evidence of areas of malignant degeneration or squamous cell carcinoma (SCC). DNA was extracted from the biopsy specimen and analyzed for human papillomavirus (HPV) DNA by hybrid capture assay
ARIA 2016: Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle (2020)

Abstract The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma and rhinitis and (3) to develop guidelines with all stakeholders that could be used globally for all countries and populations. ARIA—disseminated and implemented in over 70 countries globally—is now focusing on the implementation of emerging technologies for individualized and predictive medicine. MASK [MACVIA (Contre les Maladies Chroniques pour un Vieillissement Actif)-ARIA Sentinel NetworK] uses mobile technology to develop care pathways for the management of rhinitis and asthma by a multi-disciplinary group and by patients themselves. An app (Android and iOS) is available in 20 countries and 15 languages. It uses a visual analogue scale to assess symptom control and work productivity as well as a clinical decision support system. It is associated with an inter-operable tablet for physicians and other health care professionals. The scaling up strategy uses the recommendations of the European Innovation Partnership on Active and Healthy Ageing. The aim of the novel ARIA approach is to provide an active and healthy life to rhinitis sufferers, whatever their age, sex or socio-economic status, in order to reduce health and social inequalities incurred by the disease.
Logic Scoring of Preference (LSP) Application to Transportation Investment Portfolio Optimization: A Case Study in Colorado Springs (2013)

The evaluation and prioritization of transportation investments at the portfolio level presents a complex decision-making problem for state and regional planning organizations. Historically, transportation investment decisions have been dealt with as a series of stand-alone problems that could be resolved using straight-forward engineering solutions. In this context, improvement needs and project solutions were identified based on simple criteria, such as traffic congestion levels. Investment portfolio optimization was accomplished by listing projects in order of most to least congestion reducing, and then allocating funding to projects by rank until funding is exhausted. Recently, increasing awareness of the complex interdependencies among transportation, land-use, social, economic and ecological systems has fostered implementation of multi-criteria analysis (MCA) investment prioritization approaches that incorporate increasingly more complex goals and metrics. The simplest MCA decision model is the Weighted Sum Model (WSM). More rigorous methods, such as the Analytical Hierarchy Process (AHP) and the Technique for Ordered Preference by Similarity to Ideal Solution (TOPSIS), provide increased functionality, and support prioritization that is driven by asset performance and financial return in addition to engineering criteria. This paper examines the suitability of alternative decision models for the optimization of transportation investment priorities across full programs/portfolios. A Logic Scoring of Preference (LSP) approach is contrasted to the WSM approach that is currently used by the Pikes Peak Area Council of Governments (PPACG), as well as to an enhanced linear programming optimization (OPT) algorithm approach. Functionality, advantages, disadvantages of each method are discussed, and potential enhancements for each approach are identified.
Data from Crystal Structure of the T315I Abl Mutant in Complex with the Aurora Kinases Inhibitor PHA-739358 (2023)

&lt;div&gt;Abstract&lt;p&gt;Mutations in the kinase domain of Bcr-Abl are the most common cause of resistance to therapy with imatinib in patients with chronic myelogenous leukemia (CML). Second-generation Bcr-Abl inhibitors are able to overcome most imatinib-resistant mutants, with the exception of the frequent T315I substitution, which is emerging as a major cause of resistance to these drugs in CML patients. Structural studies could be used to support the drug design process for the development of inhibitors able to target the T315I substitution, but until now no crystal structure of the T315I Abl mutant has been solved. We show here the first crystal structure of the kinase domain of Abl T315I in complex with PHA-739358, an Aurora kinase inhibitor currently in clinical development for solid and hematologic malignancies. This compound inhibits &lt;i&gt;in vitro&lt;/i&gt; the kinase activity of wild-type Abl and of several mutants, including T315I. The cocrystal structure of T315I Abl kinase domain provides the structural basis for this activity: the inhibitor associates with an active conformation of the kinase domain in the ATP-binding pocket and lacks the steric hindrance imposed by the substitution of threonine by isoleucine. [Cancer Res 2007;67(17):7987–90]&lt;/p&gt;&lt;/div&gt;
Incapable capabilities - less is more (2022)

This document reviews existing functionalities for media capability mechanisms in the streaming media space. It shows the multitude of existing functionalities and provides an overview on what is used in practice. We provide recommendations to implementers and industry fora on how we can improve media capability signalling including focussing (extensible, yet compact) model for signalling relevant capabilities, provide a simple mapping to device APIs and support the correct implementation of capabilities on devices.
CCR7 Coordinates the Primary Immune Response by Establishing Functional Microenvironments in Secondary Lymphoid Organs (Reprinted from Cell, vol 99, pg 23-33, 1999) (2016)

The proper function of immune surveillance requires well-coordinated mechanisms in order to guide the patrolling immune cells through peripheral tissues and into secondary lymphoid organs. Analyzing gene-targeted mice, we identified the chemokine receptor CCR7 as an important organizer of the primary immune response CCR7-deficient mice show severely delayed kinetics regarding the antibody response and lack contact sensitivity and defayed type hypersensitivity reactions. Due to the impaired migration of lymphocytes, these animals reveal profound morphological alterations in all secondary lymphoid organs, Upon activation, mature skin dendritic cells fad to migrate into the draining lymph nodes. Thus, in order to bring together lymphocytes and dendritic cells to form the characteristic microarchitecture of secondary lymphoid organs, CCR7 is required to rapidly initiate an adoptive immune response.
ChemInform Abstract: Cooperative Dehydration of 1,1′,2,2′‐Ferrocenetetramethanol (I). (1992)

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.
A phase I trial of sns-314, a novel and selective pan-aurora kinase inhibitor, in advanced solid tumor patients (2009)

2536 Background: Aurora Kinases are a family of serine/threonine kinases (Aurora Kinases (AK) A, B, and C) critical for mitosis. Elevated AKs expression occurs in a high percentage of melanoma, colon, breast, ovarian, gastric, and pancreatic tumors; in a subset of these tumors the AURKA locus (20q13) is amplified. SNS-314 is a selective pan-AK inhibitor with low nanomolar IC50s. Methods: Study design is 3+3 phase 1 dose escalation by modified Fibonacci. Patients (pts) with advanced solid tumors received SNS-314 by 3 hour infusion qweek X 3 (28 day cycle). Primary endpoints: safety, tolerability, and DLT assessment. Secondary endpoints: MTD, pharmacokinetics (PK), pharmacodynamics, and antitumor activity. Pharmacodynamic endpoint was inhibition of Histone H3 phosphorylation (pHH3) evaluated by immunohistochemistry of skin punch biopsies taken pre- and 2 hours post-infusion. Results: Thirty-two pts (16M/16F; median age = 58.5 years) were enrolled into 8 cohorts: dose range 30–1800 mg/m 2 . Median cycles received =2. SNS-314 was generally well tolerated with Grade 1–2 toxicities ≥ 15% incidence: nausea (31%), fatigue (28%), vomiting, constipation, and pain (16% each), and no Grade 3+ toxicities of ≥ 15% incidence. A DLT of Grade 3 neutropenia preventing administration of all 3 doses was observed at 1440 mg/m 2 . Plasma PK were dose proportional for exposure with no accumulation of SNS-314 following weekly administration. Clearance was moderate (5.65 L/hr/m 2 , CV 39.4%); Vss approximated total body water (21.5 L/m 2 , CV 78.1%); terminal half-life was 10.4 hours (CV 66.8%). Six patients had stable disease as their best response. Inhibition of pHH3 by SNS-314 was observed in skin biopsies of patients treated at doses of 240 mg/m 2 and greater. Conclusions: SNS-314 is a novel inhibitor of AKs A, B, and C. The compound has been generally well tolerated; MTD was not established. No objective responses were observed. Pharmacodynamic activity was demonstrated by inhibition of pHH3. [Table: see text]
Formation of Highly Porous Polymeric Foams with Controlled Release Capability: A Phase-Separation Technique (2003)

The success of many tissue engineering applications depends on a scaffold with the suitable physical properties, one of which might be a macroporous structure that allows cellular ingrowth. Such a porous implant further raises the possibility of delivering chemotactic or growth factors to influence the course of cell proliferation and differentiation in situ. The scaffolds can also be preseeded with cells to accelerate tissue growth or repair. Even in the absence of these payloads, they still provide the benefit of introducing the minimal amount of foreign material into the tissue. Furthermore, by making the porous scaffold, or foam, from biodegradable polymers, the regenerated tissue would be rid of any synthetic component, leading to a more functional biological equivalent, and eliminating concerns of long-term tissue compatibility.
Interleukin-4 stimulates collagen synthesis by normal and scleroderma fibroblasts in dermal equivalents. (1991)

Interleukin-4 (IL-4) is one of the products of T-lymphocytes and mast cells, inflammatory cells which accumulate in connective tissues at early stages of fibrosis. We tested the effects of IL-4 on human fibroblasts from normal and scleroderma skin seeded in three dimensional collagen lattices ("dermal equivalents"). IL-4 (10 and 100 U/ml) stimulated collagen synthesis in a dose-dependent manner. No significant alteration of lattice retraction and cell proliferation was observed. At the concentration 100 U/ml, Il-4 was approximately twice more efficient on collagen synthesis than Transforming Growth Factor beta (10 ng/ml). IL-4 secretion in connective tissues might be an important factor for the development of fibrotic processes.
The analogy between photonic crystal fibres and step index fibres (2003)

Some properties of photonic crystal fibers quantitatively match those of standard step-index fibers, provided the right analogy is made between them, this is illustrated by calculations of second-mode cutoff (reported here for the first time to our knowledge) and propagation constants.
Mesoporous Aluminum Silicate Catalyst with Single-Type Active Sites:  Characterization by Solid-State NMR and Studies of Reactivity for Claisen Rearrangement Reactions (2006)

A mesoporous aluminum silicate (Al-MS) material has been successfully synthesized via a base-catalyzed co-condensation reaction. Solid-state NMR studies showed that the aluminum atoms are tetrahedrally coordinated and are stable up to at least 400 °C. The double resonance 27Al-29Si NMR experiment provided first direct evidence that all Al atoms are surrounded by Si atoms forming Al−O−Si bonds in the framework. The silicon to aluminum atomic ratio at the surface (Si/Al)s is estimated at around 100, which exceeds the overall Si/Al ratio of 60. Reactivity study of the mesoporous aluminosilicate shows an excellent catalytic reactivity for the Claisen rearrangement of allyl phenyl ether despite the low surface concentration of Al.
The DUAL-EVAL hardware description language and its use in the formal specification and verification of the FM9001 microprocessor (2002)

We present an introduction to the DUAL-EVAL hardware description language. DUAL-EVAL is a hierarchical, occurrence-oriented simulator for synchronous Mealy machines. We briefly describe the FM9001 microprocessor, whose design has been formally specified with the DUAL-EVAL language and mechanically proved correct with respect to a behavioral specification. The FM9001 has been fabricated as a CMOS ASIC and tested extensively.
Synthesis and properties of thermotropic polyesters modified with a non‐mesogenic rigid group (1996)

Abstract Four series of copolyesters, namely BB6‐DMT, BB5‐DMT, BB6‐DMI and BB5‐DMI series, were prepared by melt polycondensation of dimethyl 4,4′‐bibenzoate (BB) with a dimethyl phthalate (DMT: dimethyl terephthalate or DMI: dimethyl isophthalate) and an alkanediol (1,6‐hexanediol or 1,5‐pentanediol). The homopolyesters poly(hexamethylene 4,4′‐bibenzoate) (BB6) and poly(pentamethylene 4,4′‐bibenzoate) (BB5) exhibit a smectic phase. The thermotropic liquid crystalline and crystalline properties of the copolyesters are significantly influenced by the presence of the non‐mesogenic rigid phthalate unit. All BB6‐DMT copolyesters remain crystalline. As x , the molar fraction of the phthalate units in the diacid units, ≧ 0.7 the mesophase of the BB6‐DMT copolyesters is destroyed completely. For BB5‐DMT copolyesters, the mesophase disappears as x ≧ 0.4, and the copolyesters become amorphous as 0.5 ≦ x ≦ 0.8. The mesophase and the crystallinity of the BB6‐DMI copolyesters are destroyed completely as x &gt; 0.5. The BB5‐DMI copolyesters lose the mesophase as x ≧ 0.3, and become amorphous as x ≧ 0.4. The results indicate that the non‐linear isophthalate unit destroys mesophase and crystallinity of the copolyesters to a greater extent than the para ‐linked terephthalate unit.
Engineered Compounds to Control Ice Nucleation and Recrystallization (2023)

One of the greatest concerns in the subzero storage of cells, tissues, and organs is the ability to control the nucleation or recrystallization of ice. In nature, evidence of these processes, which aid in sustaining internal temperatures below the physiologic freezing point for extended periods of time, is apparent in freeze-avoidant and freeze-tolerant organisms. After decades of studying these proteins, we now have easily accessible compounds and materials capable of recapitulating the mechanisms seen in nature for biopreser-vation applications. The output from this burgeoning area of research can interact synergistically with other novel developments in the field of cryobiology, making it an opportune time for a review on this topic.