gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Benzylic Oxidation by the GifIV System. (1990)

Abstract Whereas the oxidation of benzene (I) under Gif conditions forms only traces of phenol (II) ‐ trapped as the tribromo derivative (III) ‐ the phenylmethanes (IV) produce the phenyl ketones (V).
Dieldrin–Induced Mallory Bodies in Hepatic Tumors of Mice of Different Strains (1983)

Mallory bodies (MBs) were induced in hepatic tumors by administration for up to 85 weeks of a diet containing 10 ppm dieldrin to 50 C3H/He and 62 C57BL/6J x C3H/He B6C3F1 male mice. MBs were seen in 15 of 28 (54%) mice which developed benign hepatic tumors and 33 of 45 (73%) mice with hepatocellular carcinoma, but in only 3 of 39 (8%) mice without hepatic tumors. In mice with tumors, the MBs were predominantly confined to tumor tissue and persisted in a carcinoma transplanted into a nude mouse. MBs were not observed, however, in hepatic tumors of 67 C57BL/6J, 49 C3H/He, or 81 B6C3F1 mice given 12 micrograms diethylnitrosamine i.p. on Days 0, 3, 9, and 15. Thirty-one of 195 control mice of all three strains had hepatic tumors. Only one of the controls had a tumor with an MB, and no MBs were seen in nontumor-bearing livers of controls animals. These observations, coupled with the results of a previous study in which MBs were observed in hepatocytes of dieldrin-treated C57BL/6J mice, indicate that mice treated with dieldrin are a reliable animal model for the study of MBs.
Results in the United States with Sperm Micro-Aspiration Retrieval Techniques and Assisted Reproductive Technologies (1994)

Improved methods of urological microsurgery and of various assisted reproductive technologies have resulted in the ability to achieve pregnancies with sperm aspirated microsurgically from men with bilateral congenital absence of the vasa deferentia or with ductal obstructions that cannot be surgically reconstructed. A survey was conducted of the results of such procedures performed in the United States during approximately 2 years. Female partner ovarian stimulation was initiated in 219 instances at 22 centers. Of the 219 procedures 23 (11%) were terminated without attempting any form of gamete fertilization or insemination of the wife for various reasons (no sperm or too few sperm retrieved, poor to absent sperm motility or poor quality eggs). The etiology of azoospermia in the 219 procedures was congenital absence of the vasa deferentia in 115 cases (52%), other congenital conditions in 15 (7%), failed vasectomy reversal in 37 (17%), infection in 4 (2%), other conditions (mainly ejaculatory dysfunctions that did not respond to electroejaculation and complex ductal obstructions) in 26 (12%) and not specified in 22 (10%). When only patient sperm was used pregnancy was achieved in 12 of 115 wives (10%) of those men who had congenital absence of the vasa deferentia and in 0 to 14% of the wives of men whose azoospermia was caused by other conditions. Of the 219 menstrual cycles in which ovarian stimulation was initiated pregnancy occurred in 24 (11%) with patient sperm and in 9 (4%) with donor sperm. Of these 33 pregnancies a full-term, live delivery occurred in 17 (52%), while 8 (24%) were ongoing at the time of reporting, 2 (6%) miscarried, 3 (9%) were chemical pregnancies, 1 (3%) resulted in a stillborn child and the outcome was unknown in 2 (6%). This new therapy offers only a modest chance of pregnancy. However, it affords men with azoospermia the opportunity to achieve paternity with their own sperm when other therapies are not available or applicable.
Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program (2022)

Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.
Prevalence of Endometriosis in Ovarian Cancer (2000)

Endometriosis may be the precursor of clear cell or endometrioid ovarian cancer. In this review, we focus on the prevalence of endometriosis in ovarian cancer and related clinical and epidemiological issues. According to 15 published reports, the rank order of the prevalence of endometriosis in each histologic type was clear cell (39.2%) > endometrioid (21.2%) > serous (3.3%) > mucinous type (3.0%). The high prevalence of endometriosis in clear cell and endometrioid types is a consistent finding in Japan and western countries. However, the incidence of the clear cell type is much higher (15-20% vs. 7-8%), and that of the endometrioid type is lower (7-16% vs. 18-26%), in Japan compared with western countries. This review is also concerned with the relationship between the presence of ovarian endometriosis and clinical features such as age, parity, menopausal status, clinical stage, and survival in ovarian cancer patients.
Why high-frequency pulse tubes can be tipped (2010)

Presented at the 16th International Cryocooler Conference, held May 17-20, 2008 in Atlanta, Georgia.
Disentanglement of the electronic properties of metallicity-selected single-walled carbon nanotubes (2009)

The inherent structure of single-walled carbon nanotubes (SWCNTs) provides them tremendous value as archetypical one-dimensional (1D) solids, which exhibit van Hove singularities in their local density of states, Tomonaga-Luttinger liquid behavior, ballistic transport properties, and in many other aspects, features of 1D quantum systems, which allow the study of fundamental problems. Therefore, unraveling the signature of their peculiar electronic structure as pristine material is a prerequisite for tracing any modification. Here, we show the disentanglement of the unique 1D features and bonding environments in clean metallicity sorted nanotube films. The photoemission and x-ray absorption responses unambiguously reveal how the fine structure in the C1s edge and photoemission valence band separately discerns the SWCNT metallic and semiconducting nature. This has crucial implications for applications allowing for instance finding the limit of maximum conductivity in transparent electrodes or the uniformity of power transistors, among others.
White Matter Correlates of Spoken Discourse in Cerebrovascular Disease (2022)

Abstract Background Spoken discourse (language beyond single words or sentences) performance can be used to detect cognitive impairment in cerebrovascular disease (CVD) [Roberts A, et al. (2021). Top Lang Disord 41(1):73‐98]. However, the neurological basis for altered spoken discourse in CVD is poorly defined. This study examined the association between spoken discourse and indicators of white matter microstructural integrity provided by diffusion tensor imaging (DTI) to better define the link between CVD‐related neurodegeneration and altered spoken discourse. Method Spoken discourse and 3T DTI data (30‐32 directions, b=1000) were obtained from the CVD cohort of the Ontario Neurodegenerative Disease Research Initiative (n=133). Spoken discourse analyses were completed previously [Roberts, 2021]. A DTI analysis pipeline [Hassan SMH, et al. (2019) PLoS One 14(12):e0226715] was used to generate brain maps of fractional anisotropy (FA) and mean diffusivity (MD) and calculate mean FA and MD values for the inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus – parietal (SLFp) and temporal (SLFt) endings, and uncinate fasciculi (UNC) in each hemisphere. Canonical correlation analyses examined associations between DTI metrics and 10 spoken discourse measures separately for FA in left hemisphere, MD in left hemisphere, FA in right hemisphere, MD in right hemisphere. Result Canonical correlations were significant in the left hemisphere (FA: r =0.47, p &lt;0.05; MD: r =0.51, p &lt;0.01) but not the right (FA: r =0.34, p =0.90; MD: r =0.40, p =0.15)(Figure 1). Among the white matter tracts, the strongest canonical loadings were seen for the SLFp (FA: 0.81; MD: ‐0.59) and SLFt (FA: 0.71; MD: ‐0.40) compared to the ILF (FA: 0.44; MD: 0.03) and UNC (FA: ‐0.34; MD: 0.10). Higher FA in the SLFp and SLFt was associated with better performance on measures of fluency and information content. Lower MD in these tracts was associated with better performance on measures of fluency, information content, and syntax. Conclusion Spoken discourse performance was associated with white matter microstructural integrity in the left hemisphere of the brain. Of the white matter tracts investigated in this study, impaired spoken discourse performance in CVD was most strongly linked to altered tissue microstructure in the parietal and temporal endings of the superior longitudinal fasciculus.
Performance Assessment of DP Control Systems for Different Sea States (2020)

Performances of a set of control schemes for dynamic positioning (DP) are studied in this work; DP performance is essential for future developments of autonomous shipping technology. The linear and non-linear model predictive control (MPC and NMPC), the non-linear proportional integral and derivative (NPID) control, the sliding mode control (SMC), as well as the multi-resolution PID (MRPID) control schemes, are evaluated under two different sea conditions, namely, moderate and extreme seas. Matlab/Simulink models of a full-scale ship and its corresponding scaled model are used to benchmark the efficacy of the controllers. An unscented Kalman filter (UKF) is used to estimate vessel motions and to control low frequency (LF) motions while filtering out wave frequency (WF) motions. The tuning of the controllers is also taken into consideration. Of the five controller schemes, the NMPC shows the best ability to deal with extreme disturbances efficiently. Although all of the controllers were able to maintain the ship position under moderate conditions, only the NMPC and the MRPID controllers were able to stabilize the ship under extreme sea states. Findings from this research are expected to help operators of DP systems in choosing the most effective control scheme for different sea conditions. In addition, the results are supportive of further control system development for dynamic positioning and autonomous operations of ships and offshore platforms.
Detection of Atrial fibrillation from non-episodic ECG data: A review of methods (2011)

Atrial fibrillation (A-fib) is the most common cardiac arrhythmia. To effectively treat or prevent A-fib, automatic A-fib detection based on Electrocardiograph (ECG) monitoring is highly desirable. This paper reviews recently developed techniques for A-fib detection based on non-episodic surface ECG monitoring data. A-fib detection methods in the literature can be mainly classified into three categories: (1) time domain methods; (2) frequency domain methods; and (3) non-linear methods. In general the performances of these methods were evaluated in terms of sensitivity, specificity and overall detection accuracy on the datasets from the Physionet repository. Based on our survey, we conclude that no promising A-fib detection method that performs consistently well across various scenarios has been proposed yet.
Actively mode-locked pulses from a mid-IR quantum cascade laser (2021)

The discovery of short optical pulses has triggered various breakthroughs in fundamental science and technology. While mode-locked lasers emitting visible and near-infrared light have reached a high level of maturity, methods for the generation of pulses in the mid-infrared (mid-IR) region beyond 5 µm wavelength are mostly based on non-linear downconversion of near-infrared pulses. Nowadays, quantum cascade lasers (QCLs) have become the dominant laser source in the mid-IR region [4] . In contrast to most other types of lasers, both the upper state lifetime and the gain recovery time of mid-IR QCLs are considerably shorter than the cavity roundtrip period. These properties have proven to be a major obstacle for the formation of short pulses [1] .
In vivo functional microangiography by visible-light optical coherence tomography (2014)

Although hemoglobin oxygen saturation (sO2) in the microvasculature is an essential physiological parameter of local tissue functions, non-invasive measurement of microvascular sO2 is still challenging. Here, we demonstrated that visible-light optical coherence tomography (vis-OCT) can simultaneously provide three-dimensional anatomical tissue morphology, visualize microvasculature at the capillary level, and measure sO2 from the microvasculature in vivo. We utilized speckle contrast caused by the moving blood cells to enhance microvascular imaging. We applied a series of short-time inverse Fourier transforms to obtain the spectroscopic profile of blood optical attenuation, from which we quantified sO2. We validated the sO2 measurement in mouse ears in vivo through hypoxia and hyperoxia challenges. We further demonstrated that vis-OCT can continuously monitor dynamic changes of microvascular sO2.
3‐D velocity‐independent elliptically anisotropic moveout correction (2008)

Elliptical anisotropy or lateral velocity variations can cause azimuthal variations in moveout velocity. In cases where apparent elliptically anisotropic moveout is present, a single picked velocity is inadequate to flatten an event on a 3‐D CMP gather. We propose a velocity‐independent imaging approach to perform an elliptically anisotropic moveout correction in 3‐D. The velocity‐independent approach relies on locally measured traveltime slopes rather than aggregate velocities to flatten each event and is very well suited to azimuthally variable corrections. We derive the velocity‐independent elliptically anisotropic moveout equation for the 3‐D case. We also derive expressions for extracting velocity and the angle between the symmetry and acquisition axes. Tests on synthetic and real data validate the proposed method.
Supplementary Figure S1 from Preclinical Efficacy of the Auristatin-Based Antibody–Drug Conjugate BAY 1187982 for the Treatment of FGFR2-Positive Solid Tumors (2023)

&lt;p&gt;The FGFR2-ADC BAY 1187982 inhibits microtubule polymerization resulting in induction of apoptosis.&lt;/p&gt;
Second‐order nonlinear optical response of thin films containing organic chromophores. Theoretical aspects (2000)

Abstract This paper discusses some theoretical aspects associated with the unusual second‐order nonlinear optical response of chromophoric self‐assembled stilbalzolium superlattices, and of ( N,N ‐dimethylamino)‐4‐nitrostilbene (DANS)‐doped glass polymers poled in an “in‐plane” configuration. It is found that the bulk nonlinearity of such materials strongly depends upon specific chromophore interactions. While for the stilbalzolium superlattices the supramolecular hyperpola‐rizability is strongly affected by the ion‐pair configuration, the formation of (formally) centrosymmetric charged chromophore aggregates is likely responsible for the observed anomalous strong nonlinearity in DANS‐doped in‐plane poled polymers. The simple “chromophore gas” model is thus inadequate to describe the non‐linearity of such materials.
Phytoestrogens from Genista halacsyi (Leguminosae) (2012)

The genus Genista is remarkably rich in isoflavones, which consider to be the most well studied phytoestrogens. In continuation of our research for new phytoestrogens, the aerial parts of Genista halacsyi Heldr., an endemic plant of Greece, was studied. Firstly, by classical separation methods several isoflavones were isolated namely: genistein, daidzein, biochanin, 8Meo-formononetin, isoprunetin, 3'OH-isoprunetin, genistin, 8C-glucopyranosylgenistein, 8C-glucopyranosylorobol and 8C-glucopyranosyl-4'glucopyranosylgenistein. In continuation, high-speed counter-current chromatography (HSCCC), a chromatographic technique that eliminates irreversible absorption of the sample onto solid support with an excellent sample recovery was used to isolate larger amounts. The estrogenic activity of all isolated compounds was tested using estrogen receptor-positive MCF7 and estrogen receptor-negative MDA-MB-231 cell lines. Their affinity for binding to estrogen receptors α (ERα) and β (ERβ), was also tested. In addition, we assessed their ability to promote the proliferation of estrogen receptor positive MCF7 breast carcinoma cells and the induction of Alkaline phosphatase activity in Ishikawa endometrial carcinoma cells, as well as, their ability to regulate the transcription of ERE-dependent reporter genes. We concluded that the tested compounds exhibit substantial estrogenic activity at concentrations of 1–10µM.
Evaluation of Bone Regeneration on Polyhydroxyethyl-polymethyl Methacrylate Membrane in a Rabbit Calvarial Defect Model. (2017)

This study was conducted to evaluate the capacity of guiding bone regeneration of polyhydroxyethyl-polymethyl methacrylate (PHEMA-PMMA) membrane as a guided tissue regeneration membrane for bone defects. Two 8-mm diameter transosseous round defects were made at the parietal bone of 18 New Zealand White rabbits. Defects were covered with or without PHEMA-PMMA membrane. Radiological and histological evaluation revealed that the bone tissue over the defect was more regenerated with time in both groups. However, there was significantly more bone regeneration at 8 weeks in the experimental group than the control group (p<0.05). There was no sign of membrane degradation or tissue inflammation and no invasion of muscle and fibrous tissue into defects. PHEMA-PMMA is a potential material for guided tissue regeneration membrane as it induces no adverse tissue reaction and effectively supports selective bone regeneration.
Sexual Compatibility and Taxonomy of a New Species of Epichloe Symbiotic with Fine Fescue Grasses (1994)

Mating tests among stroma-forming and nonstroma-forming strains of Epichloë from several fine fescue species, including Festuca rubra subsp. rubra and F. rubra subsp. commutata, indicated a distinct mating population of Epichloë from the Festuca hosts. Reciprocal matings of these strains with E. typhina from Dactylis glomerata, Lolium perenne and Anthoxanthum odoratum, and with a third mating population from Elymus spp. indicated complete sexual incompatibility between members of different mating populations. Two mating types, mat-1 and mat-2, were identified and shown to be segregating in exclusion in ascospore progeny, consistent with a heterothallic mating system. Based on criteria of intersterility with other known species, and the morphology of fruiting structures (size and disarticulation of ejected ascospores) a new species of Epichloë was described for which the name E. festucae is proposed. Allozyme profiles of isolates of E. festucae and of three other recognized species, E. typhina, E. baconii, and E. clarkii, emphasized genetic distinctness of the new species. Average genetic identity values between E. festucae and the other three Epichloë species ranged from 0.138 to 0.331 but was 0.872 among E. festucae isolates. All isolates of the same species were grouped in distinct, clearly separated clusters of a dendrogram.
Identification of Amino Acid Synthesis Pathways in Desulfovibrio vulgaris by Isotopic Labeling, Metabolite Analysis, and Genome Sequence Analysis (2008)

We used isotopic labeling and metabolite analyses to test the predicted amino acid synthesis pathways in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. The data suggest several pathways that were not apparent in the initial genome annotation. First, D. vulgaris synthesizes isoleucine via citramalate synthase (DVU1914). Second, D. vulgaris synthesizes methionine via O-succinyl-homoserine, cystathionine, and homocysteine. DVU0171 is a candidate for cystathionine beta-lyase, but genes for the other steps are not apparent. Third, in vitro assays confirm the presence of Re-citrate-synthase (DVU0398), which is closely related to the recently identified Re-citrate-synthase found in some Clostridia. We also propose that D. vulgaris synthesizes 3-dehydroquinate, which is required for the synthesis of aromatic amino acids, via archaeal-like transaldolase and 3-dehydroquinate cyclase/deaminase (DVU0460,DVU0461).
Computerized mammographic lesion description (2003)

This is the first report on our work to use features extracted from mammograms to classify masses by shape or by malignancy, while further study is clearly needed, our initial results are very promising.
Time of course CD64, a leukocyte activation marker, during extracorporeal circulation (2012)

CD64 is a high-affinity leukocyte receptor for the Fc portion of IgG [1]. As CD64 expression on neutrophil cells (PMNs) is upregulated specifically after bacterial stimulation, it could be used to discriminate inflammatory states from bacterial infections [1-3]. The objective was a comparison of the time course of CD64 expression on PMN cells between patients undergoing cardiac surgery with extracorporeal circulation (ECC) with septic patients.
A broadcast scheme for vehicle-to-pedestrian safety message dissemination (2017)

Ensuring cooperative awareness by periodic message beaconing in vehicular environments is necessary to address pedestrian safety. However, high periodic basic safety message broadcasting in dense vehicular environments makes accessing the communication channel very competitive. Furthermore, high-frequency periodic broadcasting causes fast device energy dissipation which is a key issue for small computing devices used in wireless sensor and mobile communications. Therefore, in order to achieve reliable message dissemination for vehicle-to-pedestrian safety, energy loss minimization mechanisms for pedestrian mobile devices should be developed. This article proposes controlling the number of broadcasts by eliminating periodic safety message broadcasts from pedestrian nodes; these nodes only receive broadcasts from vehicles and then conditionally communicate with the vehicles when safety alerts are raised. When the pedestrian nodes do not receive messages from any vehicle for a specified period, pedestrian nodes broadcast a high-priority message advertising their position. Furthermore, for the pedestrian, adaptive message emission rates and transmission duration are proposed based on defined vehicle-to-pedestrian separation distances. This approach reduces the pedestrian device energy consumption and end-to-end delay and improves the packet delivery ratio compared to the vehicular broadcast approach for safety messages defined in the IEEE 802.11 standard.