gebhart/patrepeval huggingface dataset:
Creating a common language for the subanatomy of the ovary (2022)

Dear editor, The ovary is a dynamic organ, broadly divided into anatomical structures that include the outer cortex, inner medulla, and hilum (Figure 1A and B). In addition to general proximity, these regions contain unique constituents, with differences in prevalence of certain follicle stages, relative follicle densities, blood vessels, and cell types corresponding to functional differences between structures [1]. In addition, these structures range in development, thickness, and cellular composition based on an individual’s pubertal status, menstrual cycle stage, and medical history [2]. Therefore, methods for defining subanatomic structures must account for these changes and be more adaptable than generalized descriptions of depth. Studies in the 1970s used histologic methods to characterize and infer function of cell types and anatomical structures within the ovary, however, these studies need to be integrated with ongoing work using single cell RNA-sequencing and multiplex immunofluorescent imaging to generate high-resolution maps in healthy and pathologic ovaries across the lifespan [3, 4]. These technologies will continue to expand the field’s understanding of cellular and molecular players within the ovary to inform current and future diagnostics and therapeutics. Funding agencies, such as the Chan Zuckerberg Initiative (CZI) and National Institutes of Health (NIH), have prioritized mapping human organs at the cellular level through consortiums like the Human Cell Atlas (HCA) and Human BioMolecular Atlas Program (HuBMAP; [5]). Collaboration among these consortiums and scientific community at large are critical to increase the depth, breadth, and robustness of data generated from rare human resources. Therefore, common language accounting for the complexity of ovarian subanatomy is required to identify and effectively compare data generated from diverse resources. Here, ongoing work to develop a shared nomenclature system to annotate ovarian subanatomical structures with the flexibility to support previous, ongoing, and future clinical, translational, and basic scientific research is described.
SAS, a gene amplified in human sarcomas, encodes a new member of the transmembrane 4 superfamily of proteins. (1994)

Amplification of 12q13-14 occurs in a subset of human sarcomas including malignant fibrous histiocytoma and liposarcoma. This chromosomal region has previously been found to include a number of growth-related genes including the GLI proto-oncogene and the p53-associated protein, MDM2. We now report the characterization of SAS (sarcoma amplified sequence), a novel transcript found in this region. Sequence analysis demonstrates that SAS is a novel member of a transmembrane protein family (transmembrane 4 superfamily or TM4SF) thought to be involved in growth-related cellular processes. This observation adds a TM4SF protein to the cluster of genes at 12q13-14 frequently amplified in human sarcomas.
Large-Scale Fading Precoding for Maximizing the Product of SINRs (2020)

This paper considers the large-scale fading precoding design for mitigating the pilot contamination in the downlink of multi-cell massive MIMO (multiple-input multiple-output) systems. Rician fading with spatially correlated channels are considered where the line-of-sight (LOS) components of the channels are randomly phase-shifted in each coherence block. The large-scale fading precoding weights are designed based on maximizing the product of the signal-to-interference-plus-noise ratios (SINRs) of the users, which provides a good balance between max-min fairness and sum rate maximization. The spectral efficiency (SE) is derived based on the scaled least squares (LS) estimates of the channels, which only utilize the despreaded pilot signals without any matrix inversion. Simulation results show that the two-layer large-scale fading precoding improves the SE of almost all users compared to the conventional single-layer precoding.
Nanoscale Ion-Doped Polymer Transistors (2019)

Organic transistors with submicron dimensions have been shown to deviate from the expected behavior due to a variety of so-called "short-channel" effects, resulting in nonlinear output characteristics and a lack of current saturation, considerably limiting their use. Using an electrochemically doped polymer in which ions are dynamically injected and removed from the bulk of the semiconductor, we show that devices with nanoscale channel lengths down to 50 nm exhibit output curves with well-defined linear and saturation regimes. Additionally, they show very large on-currents on par with their microscale counterparts, large on-to-off ratios of 10<sup>8</sup>, and record-high width-normalized transconductances above 10 S m<sup>-1</sup>. We believe this work paves the way for the fabrication of high-gain, high-current polymer integrated circuits such as sensor arrays operating at voltages below |1 V| and prepared using simple solution-processing methods.
Abstract 30: Global Electrical Heterogeneity on Electrocardiogram is Associated with Sudden Cardiac Death After Adjustment for Ejection Fraction (2016)

Introduction: Electrocardiographic (ECG) measures of myocardial global electrical heterogeneity (GEH) are associated with sudden cardiac death (SCD) in middle-age adults. Hypothesis: We hypothesized that time-updated ECG GEH measures are associated with SCD in elderly adults after LVEF adjustment. Methods: We analyzed data from 2 prospective cohorts: The Atherosclerosis Risk in Communities (ARIC, n=15,366; mean age 54.1±5.8 y; 44.6% male; 73.2% white) and the Cardiovascular Health Study (CHS, n=5,016; mean age 72.8±5.6 y; 43.1% male; 95.3% white). Mean spatial QRS-T angle, azimuth, elevation, and magnitude of spatial ventricular gradient (SVG), and sum absolute QRST integral (SAI QRST) were calculated from digital 12-lead ECGs and analyzed as baseline variables in ARIC and as time-updated longitudinal variables in CHS (measured yearly at 10 consecutive visits). The primary outcome was adjudicated SCD. Cox regression models were constructed: Model 1 adjusted for age, sex and race. Model 2 further adjusted for cardiovascular disease, beta-blocker use, creatinine, BMI, hypertension, diabetes, smoking, total cholesterol, HDL, triglycerides, physical activity and alcohol use. Model 3 included Model 2 variables and heart rate, QTc, LV hypertrophy and bundle branch block or intra-ventricular conduction delay. Model 4 in CHS included all Model 3 variables plus baseline LVEF and time-updated incident HF and coronary heart disease. Results: During median 13-14 y of follow-up SCD incidence was 1.51 (95%CI 1.35-1.69) per 1,000 person-yrs in ARIC, and 2.78 (95%CI 2.41-3.21) per 1,000 person-yrs in CHS. In both cohorts (Table) QRS-T angle, SVG and SAI QRST were associated with SCD. Among older adults (CHS), longitudinal SAI QRST, QRS-T angle and SVG magnitude were associated with SCD independent of LVEF. Conclusions: Baseline and longitudinal GEH ECG parameters are independently associated with SCD in middle-age and older adults, respectively. In older adults, GEH ECG parameters provide information on SCD risk beyond LVEF.
High Density Body Surface Potential Mapping with Conducting Polymer‐Eutectogel Electrode Arrays for ECG imaging (2023)

Electrocardiography imaging (ECGi) is a non-invasive inverse reconstruction procedure which employs body surface potential maps (BSPM) obtained from surface electrode array measurements to improve the spatial resolution and interpretability of conventional electrocardiography (ECG) for the diagnosis of cardiac dysfunction. ECGi currently lacks precision, which has prevented its adoption in clinical setups. The introduction of high-density electrode arrays could increase ECGi reconstruction accuracy but is not attempted before due to manufacturing and processing limitations. Advances in multiple fields have now enabled the implementation of such arrays which poses questions on optimal array design parameters for ECGi. In this work, a novel conducting polymer electrode manufacturing process on flexible substrates is proposed to achieve high-density, mm-sized, conformable, long-term, and easily attachable electrode arrays for BSPM with parameters optimally selected for ECGi applications. Temporal, spectral, and correlation analysis are performed on a prototype array demonstrating the validity of the chosen parameters and the feasibility of high-density BSPM, paving the way for ECGi devices fit for clinical application.
&lt;title&gt;Low-cost inflatable lighter-than-air remote surveillance system&lt;/title&gt; (2001)

As the size, weight, and cost of miniature electronics have continued to decrease, the feasibility of developing portable, low-cost, unmanned surveillance systems has increased tremendously in recent years. Today, manufacturers are developing small, unmanned surveillance aircraft for both military and civilian applications. However, many military, paramilitary, and civilian applications require the surveillance platform to remain stationary over a given area for extended periods. Furthermore, most current unmanned surveillance aircraft are too large to be carried by the operators in the field and require special support equipment. This paper describes the preliminary design and analysis of a lighter-than-air vehicle based surveillance system that is lightweight, portable, and will allow extended station keeping over a desired position. This new system can be applied to military surveillance and reconnaissance, border patrol/law enforcement, search and rescue, surveying, and photographic mapping.
Unusual Inversion Phenomenon of β‐Cyclodextrin Dimers in Water (2011)

A conformational analysis of three triazole-containing bridged bis-β- cyclodextrins (CD) has been carried out to evaluate their recognition ability. NMR spectroscopy and ITC measurements clearly demonstrate that one of the CD glucopyranose units undergoes a 360° rotation in water so that the spacer linking the two CDs is deeply included into one of the CD cavities. The amplitude of this inversion phenomenon depends on the nature of the spacer and results in a limited accessibility to the CD cavities in line with previous catalytic results.
Real-time improvement of LED-based photoacoustic image quality using intermittent pulse echo acquisitions (2020)

Photoacoustic imaging is a hybrid modality with advantages of both the ultrasound and optical imaging. This technique with optical spectroscopic contrast and acoustic resolution holds promise in wide range of clinical and preclinical applications. Since photoacoustic imaging also involves ultrasound detection, it is straight forward to implement pointof- care dual mode systems with capability of structural and functional imaging. High signal generated from skin-melanin layer is an important problem in any handheld reflection-mode photoacoustic probes. This problem caused by high light fluence just beneath the ultrasound probe results in reduction of vascular contrast and also causes difficulty in image interpretation. In this work, using our LED-based photoacoustic and ultrasound imaging system (AcousticX), we demonstrate the potential of using ultrasound acquisitions dynamically to suppress high photoacoustic signal from skin surface and qualitatively improve the image contrast and quality. In AcousticX, photoacoustic and conventional pulseecho acquisitions are performed in an intermittent manner resulting in a dual-mode display frame rate of 30 Hz. We make use of the line-by-line/planewave ultrasound acquisitions to automatically delineate the skin surface in quasi realtime and suppress photoacoustic signal from the identified area, resulting in improved image interpretation and contrast without losing temporal resolution. Real-time 2D and 3D (linear scan) imaging experiments were performed on finger and foot dorsum of healthy human volunteers to validate the new skin-signal suppression technique. Results give a direct confirmation that our ultrasound-assisted skin-signal reduction feature holds strong potential in enhancing vascular contrast and visual quality in real-time 2D and 3D LED-based photoacoustic imaging.
[First clinical results using a pulsed dye laser Rhodamine 590 lithotripter in treatment of ureteral calculi]. (1991)

A collaborative study about a pulsed dye laser Rhodamin 590 was undergone, 2 years ago, between the laser application center of EPFL and both urological departments of the university of Geneva and the university of Lausanne. First clinical results are presented. Ten patients have been treated for various ureteral stones, mainly calcium oxalate stones. Laser fragmentation was successful in seven cases. No serious complication was noted. Fragmentation efficiency seems better with a 320 microns fiber than with a 200 microns fiber.
The Molecular Epidemiology and Evolution of Epstein‐Barr Virus: Sequence Variation and Genetic Recombination in the Latent Membrane Protein‐1 Gene (1999)

The phylogeny and evolution of Epstein-Barr virus (EBV) genetic variation are poorly understood. EBV latent membrane protein-1 (LMP-1) gene sequences are especially heterogeneous and may be useful as a tool for EBV genotype identification. Therefore, LMP-1 sequences obtained directly from EBV-infected human tissues were examined by PCR amplification and cloning. EBV genotypes were defined as "strains" from among 22 identified LMP-1 sequence patterns. Three molecular mechanisms were identified by which genetic diversity arises in the LMP-1 gene: point mutation, sequence deletion or duplication, and homologous recombination. The rate of LMP-1 gene evolution was found to be accelerated by coinfection with multiple EBV strains. The results of this study refine our understanding of LMP-1 sequence variation and enable accurate discrimination between independent EBV infection events and the consequence of intrahost EBV evolution. Thus, this LMP-1 sequencebased approach to EBV molecular epidemiology will facilitate the study of intrahost EBV infection, coinfection, and persistence.
Involvement o f M ultiple G ene-Silencing P athways in a P aramutation-lik e P henomenon i n Arabidopsis (2015)

SUMMARY Paramutation is an epigenetic phenomenon that has been observed in a number of multicellular organisms. The epigenetically silenced state of paramutated alleles is not only meiotically stable but also ‘‘infectious’’ to active homologous alleles. The molecular mechanism of paramutation remains unclear, but components involved in RNA-directed DNA methylation (RdDM) are required. Here, we report a multi-copy pRD29A-LUC transgene in Arabidopsis thaliana that behaves like a paramutation locus. The silent state of LUC is induced by mutations in the DNA glycosylase gene ROS1. The silent alleles of LUC are not only meiotically stable but also able to transform active LUC alleles into silent ones, in the absence of ros1 mutations. Maintaining silencing at the LUC gene requires action of multiple pathways besides RdDM. Our study identified specific factors that are involved in the paramutation-like phenomenon and established a model system for the study of paramutation in Arabidopsis.
Borderlines in Borderlands (2017)

In examining how the United States gained control over the northern borderlands of Spanish America, this work reassesses the diplomacy of President James Madison. Historians have assumed Madison’s motive in sending agents into the Spanish borderlands between 1810 and 1813 was to subvert Spanish rule, but J. C. A. Stagg argues that his real intent was to find peaceful and legal resolutions to long-standing disputes over the boundaries of Louisiana at a time when the Spanish-American empire was in the process of dissolution. Drawing on an array of American, British, French, and Spanish sources, the author describes how a myriad cast of local leaders, officials, and other small players affected the borderlands diplomacy between the United States and Spain, and he casts new light on Madison’s contribution to early American expansionism.
The history of sacroiliac joint arthrodesis (2011)

The sacroiliac joint is a major weight-bearing joint interposed between the hip and the spine. Its vulnerability to injury and disease-related processes can lead to painful, irreversible changes of the sacroiliac joint, requiring surgical arthrodesis. Many surgical methods have been described for ablation of the sacroiliac joint, yet controversies surround reliable healing, imaging and confirmation of effective joint ablation. This article provides a historical review of sacroiliac joint arthrodesis techniques presented in the literature. The data are presented in three sections: overview of diagnostic methods, surgical and perioperative methods, and outcomes. A critique of each method is presented chronologically, and reasons for lack of progress or failure explored. A new method of surgical arthrodesis by calibrated distraction and grafting interposition of the joint/recess is presented.
N‐Heterocyclic Carbene Catalyzed Trifluoromethylation of Carbonyl Compounds. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Frequency-domain theory of laser infrared photothermal radiometric detection on thermal waves generated by diffuse-photon-density wave fields in turbid media (abstract) (2003)

A three-dimensional theory of the frequency-domain thermal-wave field generated inside a turbid medium with optical and thermal properties of human tissue is presented. The optical source is treated as a three-dimensional harmonically modulated diffuse photon-density wave (DPDW) field in the diffusion approximation of the radiative transfer theory. Unlike earlier Green-function-based theoretical models, exact boundary conditions are used based on the requirement that there should be no diffuse photon intensity entering the turbid medium from the outside. Explicit analytical expressions for the DPDW field and for the dependent thermal-wave field are obtained in the spatial Hankel-transform domain. The formalism is further extended to the calculation of the infrared photothermal radiometric signal arising from the nonradiatively generated thermal-wave distribution in turbid media with instantaneous nonradiative de-excitation, as well as in media with non-zero fluorescence relaxation lifetimes. Numerical inversions have been performed and presented as examples of selected special cases of the theory. It is found that the present theory with exact DPDW-field boundary conditions is valid throughout the entire domain of the turbid medium, with the exception of the very-near-surface ballistic photon “skin layer” (7–50 μm). Photothermal radiometric signals were found to be more reliably predicted than DPDW signals within this layer, due to the depth-integration nature of this detection methodology.
Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex (2004)

Transcription initiation in all three domains of life requires the assembly of large multiprotein complexes at DNA promoters before RNA polymerase (RNAP)-catalyzed transcript synthesis. Core RNAP subunits show homology among the three domains of life, and recent structural information supports this homology. General transcription factors are required for productive transcription initiation complex formation. The archaeal general transcription factors TATA-element-binding protein (TBP), which mediates promoter recognition, and transcription factor B (TFB), which mediates recruitment of RNAP, show extensive homology to eukaryal TBP and TFIIB. Crystallographic information is becoming available for fragments of transcription initiation complexes (e.g. RNAP, TBP-TFB-DNA, TBP-TFIIB-DNA), but understanding the molecular topography of complete initiation complexes still requires biochemical and biophysical characterization of protein-protein and protein-DNA interactions. In published work, systematic site-specific protein-DNA photocrosslinking has been used to define positions of RNAP subunits and general transcription factors in bacterial and eukaryal initiation complexes. In this work, we have used systematic site-specific protein-DNA photocrosslinking to define positions of RNAP subunits and general transcription factors in an archaeal initiation complex. Employing a set of 41 derivatized DNA fragments, each having a phenyl azide photoactivable crosslinking agent incorporated at a single, defined site within positions -40 to +1 of the gdh promoter of the hyperthermophilic marine archaea, Pyrococcus furiosus (Pf), we have determined the locations of PfRNAP subunits PfTBP and PfTFB relative to promoter DNA. The resulting topographical information supports the striking homology with the eukaryal initiation complex and permits one major new conclusion, which is that PfTFB interacts with promoter DNA not only in the TATA-element region but also in the transcription-bubble region, near the transcription start site. Comparison with crystallographic information implicates the PfTFB N-terminal domain in the interaction with the transcription-bubble region. The results are discussed in relation to the known effects of substitutions in the TFB and TFIIB N-terminal domains on transcription initiation and transcription start-site selection.
Development of an In Vitro Bioassay for <i>Clostridium botulinum</i> Type B Neurotoxin in Foods That Is More Sensitive than the Mouse Bioassay (1999)

A novel, in vitro bioassay for detection of the botulinum type B neurotoxin in a range of media was developed. The assay is amplified by the enzymic activity of the neurotoxin's light chain and includes the following three stages: first, a small, monoclonal antibody-based immunoaffinity column captures the toxin; second, a peptide substrate is cleaved by using the endopeptidase activity of the type B neurotoxin; and finally, a modified enzyme-linked immunoassay system detects the peptide cleavage products. The assay is highly specific for type B neurotoxin and is capable of detecting type B toxin at a concentration of 5 pg ml(-1) (0.5 mouse 50% lethal dose ml(-1)) in approximately 5 h. The format of the test was found to be suitable for detecting botulinum type B toxin in a range of foodstuffs with a sensitivity that exceeds the sensitivity of the mouse assay. Using highly specific monoclonal antibodies as the capture phase, we found that the endopeptidase assay was capable of differentiating between the type B neurotoxins produced by proteolytic and nonproteolytic strains of Clostridium botulinum type B.
Hybrid integrated sources for WDM systems (2003)

We have demonstrated an electroabsorption-modulated hybrid integrated wavelength selectable laser source comprised of a spot-size converted 1.55 /spl mu/m DFB laser array and a spot-size converted semiconductor optical amplifier/EA modulator, mounted on silicon and optically connected via silica-on-silicon waveguides. The InP components are fabricated using a novel dual-waveguide spot-size converter integration technique that produces low coupling losses and uses existing manufacturing techniques. The low chirp performance of this device makes it suitable for long-haul transmission at 2.5 Gbit/s using any of 16 50 GHz spaced channels.
Indication for Split ICSI in Our Clinic (2004)

IVFとICSIを回収された卵子の半数ずつに行うSplit ICSIを考慮すべき精液所見を検討することを目的とした．当院で初回ARTを施行した682症例の精液所見を目視法で調べ，精液濃度および運動率別の受精率，妊娠率の検討を行った．受精率30％が以下の症例では受精率50％以上の症例と比較し妊娠率は有意に低かった．精子濃度が2,000万/ml未満の症例では受精率は50.0～53.8％であり，2,000万/ml以上の症例における受精率の65.0～79.5％と比較して有意に低率であった．精子運動率が20％未満の症例では受精率は0～29.6％であり，運動率20％以上の症例の受精率66.8～76.8％と比較して有意に低率であった．精子濃度2,000万/ml未満または精子運動率が20％未満の症例に対してはsplit ICSIを考慮すべきと考えられた．