gebhart/patrepeval huggingface dataset:
Development of Immune Cells in the Intestinal Mucosa Can Be Affected by Intensive and Extensive Farm Environments, and Antibiotic Use (2018)

Epidemiological studies have demonstrated that exposure to farm environments during childhood can be linked to reductions in the incidence of immune disorders, but generating an appropriate model is difficult. 108 half-sibling piglets were born on either extensive (outdoor) or intensive (indoor) farms: at 1 day old, a subset of piglets from each litter were transferred to a high-hygiene isolator facility to create differences in rearing environment either during birth/first day or during the subsequent 56 days of life. Interactions between CD14, CD16, MHCIIDR, and capillary endothelium were assessed using four-color quantitative fluorescence immunohistology. Effects of birth and rearing environment on the antigen-presenting microenvironment of the proximal and distal jejunum (professional and stromal) were apparent at 5, 28, and 56 days after birth However, effects on CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> regulatory T-cells (T<sub>regs</sub>) in the intestinal mucosa were apparent around weaning at 28 days but had disappeared by 56 days. These T<sub>regs</sub> were reduced in the isolator piglets compared to their farm-reared siblings, but this effect was less marked in piglets born on the extensive farm and required administration of antibiotics. Our results suggest that there may be at least two windows of opportunity in which different farm environments were influencing immune development: one during the perinatal period (up to the first day of life), and one during later infancy. Furthermore, the differences on T<sub>regs</sub> suggest that the effects of early life influences may be particularly critical around weaning.
Abstract P3-06-19: Large-scale retrospective analysis between 1980-2008 in 20 838 women with breast cancer - Results in young women (&lt; 40 years old) (2013)

Abstract Background: The risk for developing breast cancer before the age of 40 is less than 1% and is similar worldwide. Breast cancer in young women is different from that of older women in terms of clinical and pathological characteristics and prognosis. We reviewed the evolution of breast cancer in young women aged &amp;lt; 40 years between 1980 and 2008 in the large database of the René Huguenin Hospital in France. Patients and Methods: Women diagnosed with a first breast cancer were prospectively included in the institution database. The analysis population included all women treated and followed between 1980 and 2008 for new breast cancer. The data were grouped into three periods: 1980-1990 (systematic pre-screening), 1991-2003 (first pilot screening experiences) and 2004-2008 (generalized systematic screening) and per age group comparing women &amp;lt;40 years and women ≥40 years. Results: From 1980-2008, there were 20838 new breast cancers diagnosed, including 1431 (6.9%) in women &amp;lt;40 years. The mean age at diagnosis in women &amp;lt;40 years remained stable throughout the entire period at 35.2 years (min-max 19-39 years). Women &amp;lt;40 years, compared to women ≥40 years, had a larger mean clinical tumor size at diagnosis (33.1 mm vs. 26.8 mm; p&amp;lt;0.0001); lower proportion of stage I tumors (28.6% vs 43.9%; p&amp;lt;0.0001); lower proportion of in situ cancers (7.6% vs 10.1%; p = 0.0034); more ductal invasive cancers (87% vs 78%; p&amp;lt;0.0001); more histological grade 3 tumors (41% vs 25%; p&amp;lt;0.0001); more HER2 overexpression (25.6% vs 10.5%; p&amp;lt;0.0001), less hormone receptor-positive phenotype (68.7% vs 80.3%; p&amp;lt;0.0001) and more triple negative phenotype (8.4% vs 5.3; p&amp;lt;0.0001). Neo-adjuvant chemotherapy was more frequent in young women (21.2% vs 7.9%; p&amp;lt;0.0001), as was adjuvant chemotherapy (47.4% vs 27.3%; p&amp;lt;0.0001). The survival rates in women &amp;lt;40 years were lower than in older women. Over the study period, among women &amp;lt; 40 years analyzed for survival, 26.3% died from breast cancer and 2.4% died from another cause; in women ≥ 40 years, 14% died from breast cancer and 10.3% died from another cause. The overall survival rate, between 1980-1990, in patients &amp;lt;40 years was 89.1% and 81.4% at 3-years and 5 years, respectively; while between 2004-2008, the overall survival rate was 96.6% and 91.4% at 3 and 5 years, respectively. Conclusion: Results of the retrospective analysis of a very large cohort of women less than 40 years diagnosed with breast cancer show that woman &amp;lt;40 years had a less favorable prognosis than older women. However, despite of not being included in screening programs, there was a substantial improvement in the prognosis for women &amp;lt;40 years over the study period between 1980 and 2008, probably due to improved treatments. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-06-19.
Negatively Charged Metal Oxide Nanoparticles Interact with the 20S Proteasome and Differentially Modulate Its Biologic Functional Effects (2013)

The multicatalytic ubiquitin-proteasome system (UPS) carries out proteolysis in a highly orchestrated way and regulates a large number of cellular processes. Deregulation of the UPS in many disorders has been documented. In some cases, such as carcinogenesis, elevated proteasome activity has been implicated in disease development, while the etiology of other diseases, such as neurodegeneration, includes decreased UPS activity. Therefore, agents that alter proteasome activity could suppress as well as enhance a multitude of diseases. Metal oxide nanoparticles, often developed as diagnostic tools, have not previously been tested as modulators of proteasome activity. Here, several types of metal oxide nanoparticles were found to adsorb to the proteasome and show variable preferential binding for particular proteasome subunits with several peptide binding "hotspots" possible. These interactions depend on the size, charge, and concentration of the nanoparticles and affect proteasome activity in a time-dependent manner. Should metal oxide nanoparticles increase proteasome activity in cells, as they do in vitro, unintended effects related to changes in proteasome function can be expected.
Monolithically-Integrated 50 Gbps 2pJ/bit Photoreceiver with Cherry-Hooper TIA in 250nm BiCMOS Technology (2019)

We report a monolithically-integrated photoreceiver with a pseudo-differential Cherry-Hooper transimpedance amplifier (TIA) in a 250nm BiCMOS process. High sensitivity 50Gbps operation in demonstrated, and the TIA architecture is analyzed.
Towards a Monolithic Cavity Soliton Laser (2009)

We propose an original design of a monolithic and integrated vertical cavity laser with saturable absorber and discuss experimental results showing the formation and fast writing/erasure of bistable laser spots.
Low-frequency noise of 90nm nFETs: hot-carrier degradation and deuterium effect (2005)

We show that the low-frequency noise (LFN) of 90 nm nFETs can increase considerably due to hot-carrier stress. Measurements reveal noise degradation for both linear and saturation regions of operation. The use of deuterium processing retards the noise degradation and improves the noise lifetime by more than 20/spl times/.
Isolation of the gal Repressor (1971)

The repressor of the galactose operon of Escherichia coli has been partially purified and identified as a protein. Induction of a lysogen in which lambda was linked to the bacterial galR and lysine genes resulted in a large increase in the production of the gal repressor. Single-step purification by affinity chromatography, using the ligand p-aminophenyl-beta-D-thiogalactoside linked to beaded agarose, provided a convenient method of separating the gal repressor from other DNA-binding proteins. Binding of gal repressor to lambdapgal[(32)P]DNA was studied by assay of binding to a nitrocellulose filter. Interaction between gal repressor and lambdapgal DNA showed a high degree of specificity; the dissociation constant of the complex was estimated to be 1.0 x 10(-12) M. Unlabeled lambdapgal DNA competed for binding to gal repressor, but lambdaDNA and lambdah80dlac DNA did not. Fucose and galactose, which function as inducers of the galactose operon in vivo, produced one-half maximal inhibition of gal repressor-lambdapgal DNA binding at concentrations of 5 x 10(-5) M.
Special issue on methods and protocols in biomedical ultrasonics [Call for Papers] (2015)

Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.
Pemphigus autoantibodies generated through somatic mutations target the desmoglein-3 cis-interface (2012)

Pemphigus vulgaris (PV) is an autoimmune blistering disease of skin and mucous membranes caused by autoantibodies to the desmoglein (DSG) family proteins DSG3 and DSG1, leading to loss of keratinocyte cell adhesion. To learn more about pathogenic PV autoantibodies, we isolated 15 IgG antibodies specific for DSG3 from 2 PV patients. Three antibodies disrupted keratinocyte monolayers in vitro, and 2 were pathogenic in a passive transfer model in neonatal mice. The epitopes recognized by the pathogenic antibodies were mapped to the DSG3 extracellular 1 (EC1) and EC2 subdomains, regions involved in cis-adhesive interactions. Using a site-specific serological assay, we found that the cis-adhesive interface on EC1 recognized by the pathogenic antibody PVA224 is the primary target of the autoantibodies present in the serum of PV patients. The autoantibodies isolated used different heavy- and light-chain variable region genes and carried high levels of somatic mutations in complementary-determining regions, consistent with antigenic selection. Remarkably, binding to DSG3 was lost when somatic mutations were reverted to the germline sequence. These findings identify the cis-adhesive interface of DSG3 as the immunodominant region targeted by pathogenic antibodies in PV and indicate that autoreactivity relies on somatic mutations generated in the response to an antigen unrelated to DSG3.
Additive—additive interaction: A study of the ep and AW performance of sulphurised jojoba oil and sulphurised xanthate in the presence of mocontaining friction modifiers (1998)

Abstract The extreme‐pressure (EP) and antiwear (AW) performance of three soluble molybdenum compounds (commercial molybdenum dialkyldithiophosphate, commercial molybdenum dialkyl dithiocarbamate, and synthesised molybdenum dialkyl dithiocarbamate), and two sulphur‐containing EP compounds (sulphurised jojoba oil and sulphurised O‐stearyl‐S‐oleyl xanthate) have been studied alone and in combination, using a four‐ball tester. The behaviour of the additives in combination has been found to be selective, and dependent on the chemistry and ratio of the additive components. In general, the addition of Mo‐type friction modifiers (FM) to sulphurised EP compounds has shown a synergism, of varying order, in their EP and AW properties.
Mapping of Heterogeneous Catalyst Degradation in Polymer Electrolyte Fuel Cells (2020)

Durability of cathode catalyst in polymer electrolyte fuel cells (PEFCs) is a key factor, limiting large-scale commercialization of PEFC for transportation applications. The catalyst degradation occurs during operational load profiles switches from ideal to peak, where multiple operational factors affect the degradation rate. The catalyst degrades heterogeneously as the catalyst particles are exposed to local variations throughout the entire catalyst layer during operation. State-of-the-art analytical techniques for studying degradation of Pt catalyst do not possess fine spatial resolution to elucidate such non-uniform degradation behavior at a large electrode level. We report a new methodology to spatially resolve and quantify the heterogeneous Pt catalyst degradation over a large area (several cm 2 ) of aged MEAs based on synchrotron X-ray micro-diffraction. PEFC samples were aged using voltage cycling as an accelerated stress test. The heterogeneity of catalyst degradation at a micrometer length scale was visualized by mapping Pt catalyst particle size after voltage cycling between 0.6V and open circuit potential. We demonstrated in details that the Pt catalyst particle size growth was non-uniform and followed the flow field geometry. The Pt particle size growth was greater in the area under the flow field land, while it was minimal in the area under the flow field channel. Additional non-uniformity was observed with the Pt particle size increasing more rapidly at the gas outlet area of than the Pt particle size at the inlet area. Figure 1
Transparent conducting oxide clad limited area epitaxy semipolar III-nitride laser diodes (2016)

The bottom cladding design of semipolar III-nitride laser diodes is limited by stress relaxation via misfit dislocations that form via the glide of pre-existing threading dislocations (TDs), whereas the top cladding is limited by the growth time and temperature of the p-type layers. These design limitations have individually been addressed by using limited area epitaxy (LAE) to block TD glide in n-type AlGaN bottom cladding layers and by using transparent conducting oxide (TCO) top cladding layers to reduce the growth time and temperature of the p-type layers. In addition, a TCO-based top cladding should have significantly lower resistivity than a conventional p-type (Al)GaN top cladding. In this work, LAE and indium-tin-oxide cladding layers are used simultaneously in a (202¯1) III-nitride laser structure. Lasing was achieved at 446 nm with a threshold current density of 8.5 kA/cm2 and a threshold voltage of 8.4 V.
Wireless Vibrotactile Trainer for Balance Rehabilitation (2009)

During balance rehabilitation, physical therapists typically provide verbal instruction and/or physically reposition a patient to demonstrate proper postural position and movements. We have developed a wireless device that enables an expert (such as a physical therapist) to map his/her movements to a trainee in a hands-free fashion. The trainee is subsequently able to mimic the motion of the expert by interpreting positional cues presented via vibrotactile feedback to the relevant body segments. This device will potentially enable a therapist to aid multiple patients simultaneously and/or remotely, or enable a trainee (such as an athlete or student) to replicate expert movements. The device comprises an Expert Module (EM) and Trainee Module (TM). Both the EM and TM are composed of six degree-of-freedom inertial measurement units, microcontrollers, and batteries. The TM also has an array of vibrating actuators that provides the user with vibrotactile biofeedback. The expert dons the EM, and his/her relevant body position is computed by an algorithm based on an extended Kalman filter that provides asymptotic state estimation. The captured body position information is transmitted wirelessly to the trainee, and directional instructions regarding the desired motion/position are displayed via vibrotactile feedback. The trainee is instructed to move in the direction of the vibration sensation until the vibration is eliminated. While prior work has demonstrated the use of vibrotactile stimulation for improved motor learning, this portable and wireless device is suitable for use outside of a laboratory environment. Five healthy young blindfolded subjects were instructed to mimic recorded expert anterior-posterior trunk tilt motion using the aforementioned device in a series of proof-of-concept studies designed to investigate the effects of changing the feedback activation threshold and varying the nature of the feedback. To characterize the efficacy of the system, we performed a cross correlation of expert and trainee trunk tilt angle while varying the threshold angle difference at which vibrotactile feedback was applied. Preliminary results showed that subjects performed best at 0.5 and 0.75 degree thresholds among those tested (0.5, 0.75, 1.0, 1.25, 1.5). The normalized mean cross correlations for the 0.5 and 0.75 threshold conditions were 0.96 and 0.97 respectively, while the mean differences between expert and trainee trunk tilt angles were 1.1 and 1.2 degrees respectively. Further studies at 0.5 and 0.75 threshold conditions confirmed that proportional plus derivative feedback of the angle difference resulted in superior performance compared to proportional or derivative feedback alone. Repetition of the task was not significant suggesting that trainees could immediately use the device to accurately replicate expert anterior-posterior trunk tilt movements.
Role of autonomous androgen receptor signaling in prostate cancer initiation is dichotomous and depends on the oncogenic signal (2011)

The steroid hormone signaling axis is thought to play a central role in initiation and progression of many hormonally regulated epithelial tumors. It is unclear whether all cancer-initiating signals depend on an intact hormone receptor signaling machinery. To ascertain whether cell autonomous androgen receptor (AR) is essential for initiation of prostate intraepithelial neoplasia (PIN), the response of AR-null prostate epithelia to paracrine and cell autonomous oncogenic signals was assessed in vivo by using the prostate regeneration model system. Epithelial-specific loss of AR blocked paracrine FGF10-induced PIN, whereas the add back of exogenous AR restored this response. In contrast, PIN initiated by cell-autonomous, chronic-activated AKT developed independent of epithelial AR signaling. Our findings demonstrate a selective role for AR in the initiation of PIN, dependent on the signaling pathways driving tumor formation. Insights into the role of hormone receptor signaling in the initiation of epithelial tumors may help define this axis as a target for chemoprevention of carcinomas.
Frequency-resolved measurements of hemodynamic oscillations and quantitative analysis with a novel hemodynamic model (2013)

We present frequency-resolved measurements of the amplitude and phase of cerebral hemodynamic oscillations associated with paced breathing and measured with near-infrared spectroscopy on the forehead of a human subject. We have performed measurements at eleven paced breathing frequencies in the range 0.07-0.25 Hz. The resulting frequency spectra of the amplitude and phase of the hemodynamic oscillations were fit with a recently developed hemodynamic model,<sup>1</sup> that was able to reproduce the measured spectra and to determine a number of associated physiological parameters. The parameters measured include the blood transit times in the capillary (0.87 s) and venous (1.0 s) compartments, and the high-pass cutoff frequency of cerebral autoregulation (0.087 Hz). We also illustrate the implications of the new hemodynamic model on the basis of a phasor representation of physiological and hemodynamic oscillations. The combination of frequency-resolved measurements of cerebral hemodynamics and the phasor-based, frequency-domain solution of the new hemodynamic model provides a novel tool for cerebral hemodynamic studies with a potential for assessing a variety of physiological, functional, and pathological conditions.
Entanglement versus gap for one-dimensional spin systems (2010)

We study the relationship between entanglement and spectral gap for local Hamiltonians in one dimension. The area law for a one-dimensional system states that for the ground state, the entanglement of any interval is upper-bounded by a constant independent of the size of the interval. However, the possible dependence of the upper bound on the spectral gap Delta is not known, as the best known general upper bound is asymptotically much larger than the largest possible entropy of any model system previously constructed for small Delta. To help resolve this asymptotic behavior, we construct a family of one-dimensional local systems for which some intervals have entanglement entropy which is polynomial in 1/Delta, whereas previously studied systems, such as free fermion systems or systems described by conformal field theory, had the entropy of all intervals bounded by a constant times log(1/Delta).
Quaternary Carbon Centers by Cinchonine-Catalyzed Mannich Reactions (2006)

Herein, the scope of the cinchona alkaloid catalyzed Mannich reaction has been expanded. Also α-quaternary β-amino esters (acids) can now be prepared. Employing cyclic β-diketones 2 as the nucleophile and several acyl imines 3 as the electrophile, cinchonine (1) promoted the formation of β-keto ester products 4 in high yields (90-98%), diastereoselectivities (90-99% de) and enantioselectivities (90-99%). In addition, aryl-propenyl acyl imines 3 (R3= CH=CHAr) could be introduced as a new class of electrophiles for this reaction. The high selectivity of the catalyst is explained by its bifunctionality: the quinoline ring is able to shield the si-face of the enolized β-diketone, which can only be enolized if there is a hydroxyl group present in the catalyst.
Intraoperative OCT Imaging of the Argus II Retinal Prosthesis System (2016)

Intraoperative imaging of the Argus II electrode array is feasible and provides information about electrode array-retina interface and distance to help guide a surgeon. Microscope integration of OCT appears to provide an optimal and efficient approach to intraoperative OCT during Argus II array placement. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:999-1003.].
Newer Anesthesia and Rehabilitation Protocols Enable Outpatient Hip Replacement in Selected Patients (2009)

Level IV, therapeutic study. See the Guidelines for Authors for a complete description of levels of evidence.
Suppression of MHC class I antigens in oncogenic transformants: association with decreased recognition by cytotoxic T lymphocytes. (1996)

Cytotoxic T lymphocytes (CTLs) recognize peptide fragments derived from endogenous proteins, processed internally, and presented at the cell surface by major histocompatibility complex (MHC) class I molecules. The use of specific CTL for cancer therapy is limited because of their dependence on effective processing and presentation of appropriate antigenic peptides. Structural alterations, like point mutation or somatic loss, or dysregulation of key elements in the processing or presentation pathway, may allow cells to escape the immune surveillance. Indeed, the expression of MHC class I antigens on the surface of virus- and oncogene-transformed cells is low and correlates with tumorigenicity. Transformation of murine fibroblasts with the ras oncogene results in the suppression of cell surface expression of all H-2 loci as determined by FACScan analysis using a panel of monoclonal antibodies. We then examined whether the oncogene-mediated suppression of MHC class I surface expression was associated with reduced recognition of transformants by CD8+ T lymphocytes. Murine T lymphoma cells were stably transfected by the Ha-ras oncogene. The transfectants expressed distinct levels of the Ha-ras specific protein p21. Again, immunofluorescence analysis demonstrated an inverse correlation between oncogene and MHC class I surface expression in RMAras transformants. Allogeneic H-2Kb-restricted cytotoxic T lymphocytes were able to efficiently lyse the parental T lymphoma cells. In contrast, the CTL-mediated lysis of ras transformants was significantly downregulated compared with untransfected RMA cells. The efficiency of CTL-mediated lysis of RMAras cells was directly associated with reduced MHC class I membrane and high p21ras protein expression. Thus, the oncogene-mediated downregulation of MHC class I surface expression resulted in a reduced CTL response. Attempts are in progress to revert the defects in MHC class I surface expression of oncogenic transformants by introducing the different elements of the antigen presentation pathway. Such studies will not only provide improved understanding of the mechanisms of tumor escape, but also will suggest strategies to repair cellular defects in cancer patients having impaired expression of MHC class I antigens.