gebhart/patrepeval huggingface dataset:
Regression of Abdominal Fat in Broilers on Abdominal Fat in Spent Parents (1982)

A total of 261 pedigreed broilers out of 10 sires and 27 dams from a high fat line and 378 pedigreed broilers out of 11 sires and 34 dams from a low fat line were probed in the vent at 8 weeks of age as an indirect measure of abdominal fat. The broilers were weighed alive, slaughtered, and eviscerated. Abdominal fat, eviscerated carcass without giblets, and carcass shell weights were taken for each chicken. The correlations between caliper measurements and abdominal fat were below +.2. The sires and dams of the two lines were weighed alive at 14 months of age, slaughtered, eviscerated, and the same carcass measurements taken as for their broiler progeny. Sixteen of 21 sires had no measurable abdominal fat. The dams averaged 3.44% abdominal fat of live body weight compared with 1.55% for their female broiler progeny. The coefficient of variation for abdominal fat as a percentage of live weight of dams was 28%. Regressions of daughters and sons on midpoint of parents for abdominal fat as a percentage of live weight was +.305 and +.204, respectively, and were significant (P≤.05). The regression of daughters on dams and of sons on dams for abdominal fat as a percentage of live weight was +.186 and +.154, respectively, and both were significant (P≤.01).
Abstract 3639: Senescent stromal cells drive breast cancer tumorigenesis (2022)

Abstract Age is the largest risk factor for the development of cancer, including breast cancer, which is the most frequent malignancy in women. Investigation into how age impacts breast cancer development suggests that both the accumulation of oncogenic mutations within incipient tumor cells and age-related stromal changes conspire to drive tumorigenesis. While numerous physiologic changes arise with age, we posit that the accumulation of p16INKA4 (p16) positive senescent cells, which express various cytokines, chemokines, and enzymes collectively referred to as the senescence-associated secretory phenotype (SASP) contribute to cancer progression. SASP factors not only directly promote the proliferation of tumor cells, but also create an immunosuppressive microenvironment that contributes to robust tumor growth. Immunosuppressive SASP factors are detectable in human breast cancer stroma and high p16 positivity in stromal cells strongly correlates with breast cancer recurrence regardless of subtype. To investigate the role of senescent stroma in mammary tumor development, we crossed MMTV-PyMT (PyMT) transgenic mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16-positive cells. Depletion of senescent stromal cells in PyMT/INK mice led to significantly delayed mammary tumor onset and changes in various tumor-infiltrating immune cell populations. Analyses of single-cell RNA-sequencing (scRNA-seq) datasets of murine and human mammary tumor/breast cancer samples revealed that senescence is restricted to a cancer-associated fibroblasts (CAFs) subpopulation, which expresses high levels of immune-related and extracellular matrix (ECM)-related SASP factors and shows decreasing abundance in PyMT/INK mice upon the depletion of senescent stroma. Together, these data suggest that senescent CAFs contribute to mammary gland tumorigenesis by modulating tumor immunity and remodeling ECM in the microenvironment. Citation Format: Jiayu (Jennifer) Ye, Ana Paula Delgado, Scott Powers, Sheila Stewart. Senescent stromal cells drive breast cancer tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3639.
Bi-Axial Stress Effects On Barkhausen-Noise (2015)

Mechanical stress has a strong effect on the magnitude<br> of the Barkhausen-noise in structural steels. Because the<br> measurements are performed at the surface of the material, for a<br> sample sheet, the full effect can be described by a biaxial stress field.<br> The measured Barkhausen-noise is dependent on the orientation of<br> the exciting magnetic field relative to the axis of the stress tensor.<br> The sample inhomogenities including the residual stress also<br> modifies the angular dependence of the measured Barkhausen-noise.<br> We have developed a laboratory device with a cross like specimen<br> for bi-axial bending. The measuring head allowed performing<br> excitations in two orthogonal directions. We could excite the two<br> directions independently or simultaneously with different amplitudes.<br> The simultaneous excitation of the two coils could be performed in<br> phase or with a 90 degree phase shift. In principle this allows to<br> measure the Barkhausen-noise at an arbitrary direction without<br> moving the head, or to measure the Barkhausen-noise induced by a<br> rotating magnetic field if a linear superposition of the two fields can<br> be assumed.
The Measurement of pO2 by O2 Electrode in the Presence of Changing pCO2 (1983)

Studies on the transport of O2 and CO2 in the alveoli and blood have focused on simultaneous measurements of the two gases with classical instruments; an interaction between the two gases has been assumed (see Bohr Effect and Rahn-Otis Plot). Nevertheless, of late years with wide use of the Kimmich-Kreuzer Oxygen Electrode in liquids and gases, the measurements have included oxygen alone. These small (2mm) polarographic catheter electrodes have been used in both physiologic and bioengineering applications. Within a particular range of polarization voltage, the electrode current is limited by O2 diffusion across a membrane; i.e., at a constant polarization voltage, current is linearly related to pO2. Since it is often the case that measurements of pO2 are taken while pCO2 is changing, CO2 effects on the electrode current should be known and corrected for. In the present experiments, electrical currents at 5% and 21% O2 with varying amounts of CO2 were measured. Polarograms (a plot of current v. voltage) made in the presence and absence of CO2 were compared. The pO2 measurement is significantly affected by CO2 at 21% O2, but not a 5% O2; i.e., the O2 value changed with different CO2 levels. These results are particularly interesting since the electrode membrane is a physical model of the alveolar membrane.
The Yin and Yang of Integrin Function in Re-Epithelialization During Wound Healing (2013)

This work provides knowledge that leads to the understanding of delayed re-epithelialization during wound healing and dermal epidermal defects, blistering, and chronic skin diseases, hence providing the opportunity to understand the basic cellular and molecular mechanisms involved in these situations.
Calcium limits substrate accessibility or reactivity at the manganese cluster in photosynthetic water oxidation (1991)

The structural changes which the tetramanganese cluster responsible for catalyzing photosynthetic water oxidation undergoes upon calcium depletion of photosystem II membranes via the citrate extraction method has been further characterized. The modified multiline EPR signal which forms has been further identified with an S2' oxidation state. The increased number of hyperfine lines (at least 26) and 25% narrower hyperfine splittings from 55Mn versus the normal S2-state signal indicate a redistribution of spin density, most likely within a spin-coupled tetranuclear Mn cluster. A simpler binuclear Mn description for this signal can be eliminated. Slow conformational changes occur over 30 min which cause subtle changes in the hyperfine structure. Comparison to the modified multiline signals produced by Sr2+ replacement of Ca2+ and NH3-treated PSII reveal similarities suggestive of formation of the same spin S = 1/2 state. Substrate accessibility in the dark S1' state, measured as Mn2+ release upon incubation with NH2OH, is increased by 10-fold over calcium-containing PSII centers. Diphenylcarbazide, an efficient electron donor to Tyr-Z+ only in PSII membranes in which Mn is removed or dislocated, was found to donate electrons in Ca(2+)-depleted PSII, indicating altered accessibility or reactivity. These results suggest a possible "gatekeeper" role for Ca2+ in limiting access of substrate water to the Mn cluster. These changes are not due to release of the three extrinsic polypeptides of PSII which remain bound. Citrate treatment also causes partial air oxidation of the reaction-center Fe2+ ion, associated with the quinone electron acceptors. The resulting Fe3+ possesses an EPR signal at g = 4.37 arising from conversion to a rhombic symmetry ligand field.
Supplementary Figure 4 from MDA-9/Syntenin and IGFBP-2 Promote Angiogenesis in Human Melanoma (2023)

&lt;p&gt;PDF file - 198K, Expression of different angiogenic factors in MDA-9/Syntenin expressing clones.&lt;/p&gt;
Genomic diversity of small round structured viruses in the United Kingdom (1994)

Fifty-two faecal specimens collected in the United Kingdom between 1986 and 1992, which contained small round structured virus (SRSV) particles, were tested by reverse transcriptase polymerase chain reaction assays using two primer pairs derived from sequences of Snow Mountain Agent and Norwalk virus. There was poor correlation between results obtained with each primer pair. Twenty specimens (38%) gave positive bands with SM51/31 primers and 18 (34%) were positive with SM52/32 primers, with a total of 30 specimens (57.7%) giving amplification products of the expected size with one or both primer pairs. Genomic variation was investigated by sequencing a 266 bp region of the RNA polymerase gene from nine strains which had been antigenically typed by solid phase immune electron microscopy (SPIEM). RNA sequence identities ranged from 53 to 99%. Three genomic groups were suggested by phylogenic analysis, the first of which contained Norwalk virus, Southampton virus, and strains typed by SPIEM as SRSV UK2. The second contained Snow Mountain agent and strains typed as either SRSV UK3 or UK4. The third contained strains typed as SRSV UK1 and strains untypeable by SPIEM. Some correlation was demonstrated when antigen typing by SPIEM and phylogenic grouping based on sequence data were compared.
Human cingulate cortex: Surface features, flat maps, and cytoarchitecture (1995)

The surface morphology and cytoarchitecture of human cingulate cortex was evaluated in the brains of 27 neurologically intact individuals. Variations in surface features included a single cingulate sulcus (CS) with or without segmentation or double parallel sulci with or without segmentation. The single CS was deeper (9.7 +/- 0.81 mm) than in cases with double parallel sulci (7.5 +/- 0.48 mm). There were dimples parallel to the CS in anterior cingulate cortex (ACC) and anastomoses between the CS and the superior CS. Flat maps of the medial cortical surface were made in a two-stage reconstruction process and used to plot areas. The ACC is agranular and has a prominent layer V. Areas 33 and 25 have poor laminar differentiation, and there are three parts of area 24: area 24a adjacent to area 33 and partially within the callosal sulcus has homogeneous layers II and III, area 24b on the gyral surface has the most prominent layer Va of any cingulate area and distinct layers IIIa-b and IIIc, and area 24c in the ventral bank of the CS has thin layers II-III and no differentiation of layer V. There are four caudal divisions of area 24. Areas 24a' and 24b' have a thinner layer Va and layer III is thicker and less dense than in areas 24a and 24b. Area 24c' is caudal to area 24c and has densely packed, large pyramids throughout layer V. Area 24c' g is caudal to area 24c' and has the largest layer Vb pyramidal neurons in cingulate cortex. Area 32 is a cingulofrontal transition cortex with large layer IIIc pyramidal neurons and a dysgranular layer IV. Area 32' is caudal to area 32 and has an indistinct layer IV, larger layer IIIc pyramids, and fewer neurons in layer Va. Posterior cingulate cortex has medial and lateral parts of area 29, a dysgranular area 30, and three divisions of area 23: area 23a has a thin layer IIIc and moderate-sized pyramids in layer Va, area 23b has large and prominent pyramids in layers IIIc and Va, and area 23c has the thinnest layers V and VI in cingulate cortex. Area 31 is the cinguloparietal transition area in the parasplenial lobules and has very large layer IIIc pyramids. Finally, variations in architecture between cases were assessed in neuron perikarya counts in area 23a. There was an age-related decrease in neuron density in layer IV (r = -0.63; ages 45-102), but not in other layers.(ABSTRACT TRUNCATED AT 400 WORDS)
Calculation of beta dosimetry in radiation synovectomy using Monte Carlo simulation (EGS4) (1993)

Using the EGS4 Monte Carlo code, absorbed dose rate factors were estimated for four radionuclides of interest in radiation synovectomy, an intra-articular radiation therapy to treat rheumatoid arthritis. The treatment consists of the injection of a beta-emitting radionuclide into the joint capsule in order to eliminate diseased synovium through irradiation. The radionuclides investigated are 32P, 90Y, 165Dy, and 198Au. Calculations reveal the absorbed dose factor (cGy cm2/MBq s) as a function of distance (mm) in an EGS4 model of the rheumatic joint. The model incorporates bone, articular cartilage, joint capsule, and tissue (synovium) components found in all synovial joints, with dimensions in the model corresponding to dimensions typically found in larger joints, e.g., the knee, shoulder, or hip. Results are compared with previous, analytical approaches to beta dosimetry in radiation synovectomy. In addition, radiation backscatter due to the presence of bone is investigated and determined to have a negligible enhancement effect on absorbed dose to synovium.
Digit ratios (2D:4D) determined by computer‐assisted analysis are more reliable than those using physical measurements, photocopies, and printed scans (2009)

Prenatal androgens influence the second to fourth digit ratio (2D:4D) of hands with men having lower ratios than women. Numerous methods are used to assess 2D:4D including, physical measurements with calipers, and measurements made from photocopies, scanned images, digital photographs, radiographs, and scaled tubes. Although each method appears relatively reliable, agreement upon a gold standard is necessary to better explore the putative effects of prenatal androgens. Our objective was to assess the level of intra and interobserver reliability when evaluating 2D:4D using four techniques: (1) physical measurements, (2) photocopies, (3) printed scanned images, and (4) computer-assisted image analysis. Physical measurements, photocopies, and printed scanned images were measured with Vernier calipers. Scanned images were also measured with computer-based calipers. Measurements were made in 30 men and 30 women at two different time points, by three experienced observers. Intraclass correlation coefficients were used to assess the level of reliability. Intraobserver reliability was best for computer-assisted (0.957), followed by photocopies (0.939), physical measurements (0.925), and printed scans (0.842; P = 0.015). Interobserver reliability was also greatest for computer-assisted (0.892), followed by photocopies (0.858), physical measurements (0.795), and printed scans (0.761; P = 0.001). Mean 2D:4D from physical measurements were higher than all other techniques (P < 0.0001). Digit ratios determined from computer-assisted, physical measurements, and printed scans were more reliable in men than women (P = 0.009, P = 0.017, and P = 0.012, respectively). In summary, 2D:4D determined from computer-assisted analysis yielded the most accurate and consistent measurements among observers. Investigations of 2D:4D should use computer-assisted measurements over alternate methods whenever possible.
Magnetic Fluid Seals for Special Applications (1980)

Three magnetic fluid seals custom engineered to meet specific application objectives are discussed. These seals are: a belt edge seal, a large diameter seal and a centrifugal seal. Extensive experimental data were acquired on the first two seals to determine their performance characteristics. Some of these test results are compared with the theoretical expectations. Numerical computations are made on the centrifugal seal to Predict its sealing capabilites.
Molecular characterization of antithrombin III (ATIII) variants using polymerase chain reaction. Identification of the ATIII Charleville as an Ala 384 Pro mutation. (1989)

The genes of seven structural mutants of antithrombin III (ATIII), presenting either defective serine protease reactivity or abnormal heparin binding, were analyzed. The polymerase chain reaction (PCR) was used to amplify the corresponding gene exon and the mutation was identified by either dot blot analysis using a battery of allele-specific oligonucleotide probes or sequencing. Variants Paris and Paris 2 were identified as Arg 47 Cys mutations, and Clichy, Clichy 2, and Franconville were found to be Pro 41 Leu mutations. All five are heparin binding-site variants. ATIII Avranches is an Arg 393 His mutation and ATIII Charleville is an Ala 384 Pro mutation. These two mutations impair the reactive site of the molecule. ATIII Charleville is a new mutation of the reactive center, as predicted by previous biochemical data. The position of this new mutation, together with the other previously described mutations of the reactive center, sheds light on the molecular function of this site in inhibiting thrombin. Finally, genomic amplification by PCR is a powerful technique for the fast identification of antithrombin III mutations and their homozygous/heterozygous status, and should be useful for predicting thrombotic risk.
Dietary boron and fish oil have desirable effects on vertebral microarchitecture and strength (2006)

Nutritional amounts of boron (B) and fish oil (FO) beneficially affect long bone histomorphological and gross physical characteristics. Thus, an experiment was performed to determine whether B deprivation and FO instead of safflower oil (SO) in the diet would change vertebral microarchitecture and strength. Female rats were fed diets containing 0.1 mg B/kg in a factorial arrangement with variables of supplemental B at 0 (B‐def) or 3 (B‐adq) mg/kg and fat sources of 75 g SO/kg or 65 g FO (menhaden oil)/kg plus 10 g linoleic acid/kg (added to assure adequacy of n‐6 fatty acids). After 6 weeks, 6 females per treatment were bred. Dams and pups continued on their respective diets through gestation, lactation and after weaning. Femurs for mineral analysis and vertebrae for examination by microcomputed tomography were collected from 15 and 12 males per group, respectively, at age 21 wk. Rats fed the B‐def diet exhibited deficiency signs of decreased femur B concentrations and body weight. Vertebral trabecular separation and structural model index were increased and trabecular bone volume fraction was decreased by B‐def. Trabecular thickness was decreased by B‐def with the effect more marked when SO was fed. Trabecular cross sectional area was increased by FO. Finite element analysis indicated that the force required to compress the vertebral core was increased (P&lt;0.05) by FO and tended (P&lt;0.08) to be decreased (1929 vs 1595 N) by B‐def. The findings show that FO and B have synergistic favorable effects on vertebral microarchitecture and strength. (Supported by in‐house USDA &amp; Okla. Agric. Expt. Station funds)
In‐season docosahexaenoic acid supplementation does not prevent white matter damage during a single American football season: Implications for neurodegeneration prevention (2022)

Abstract Background Repetitive sub‐concussive head impacts (RSHIs) are common in American football, result in changes to white matter microstructural integrity, and are suggested as a potential risk factor for neurodegenerative diseases, including Alzheimer’s disease. RSHI‐induced white matter degradation may accelerate neurodegenerative processes, necessitating effective preventative and therapeutic approaches in this population. Prior studies indicate potential neuroprotective and remyelinating effects of docosahexaenoic acid (DHA). Here, we conducted a double‐blind, randomized, placebo‐controlled trial to assess the effects DHA supplementation during a National Collegiate Athletic Association football season on neuroimaging measures of white matter integrity. Method Thirty‐eight participants were randomized to treatment (6g DHA/EPA) or placebo (6g oleic/linoleic acid) group for seven months of five‐times‐per‐week supplementation. 27 participants completed the trial and had complete neuroimaging datasets ( n = 16 placebo; n = 11 treatment). White matter integrity changes from preseason to immediately post‐season were quantified using voxel‐wise fractional anisotropy and diffusivity (mean, axial, radial) as well as deterministic tractography using quantitative anisotropy (QA). Gray matter volume as well as intra‐regional, edge‐wise, and network level functional connectivity were obtained as secondary measures along with serum neurofilament light (NfL) as a peripheral biomarker of axonal damage. Result There were no voxel‐wise, between‐group differences in voxel‐wise DTI analyses. Compared to placebo, the treatment group had increased QA in ascending corticostriatal fibers and decreased QA in long association and commissural fibers. Increased mean (ρ = 0.47), axial (ρ = 0.44), and radial (ρ = 0.51) diffusivity and decreased QA (ρ = ‐0.52) in the corpus callosum and bilateral corona radiata were correlated with increasing NfL levels during the season irrespective of treatment group. Default mode/frontoparietal network connectivity ( g = 0.96, p = 0.024) was greater in the treatment group. Conclusion In‐season DHA supplementation was insufficient to prevent or protect against axonal damage as it occurred during the season. However, there may be neuroprotective effects on functional connectivity despite structural damage. If RSHIs are a risk factor for future neurodegeneration, then alternative therapeutic merit further investigation. These present outcomes do not support the use of in‐season DHA supplementation as a preventive strategy to reduce brain injury resulting from collegiate football. Acknowledgement Study funded by the Center for Innovation in Brain Science, University of Arizona. DHA provided by Pharmavite
Optimization of Conditions for Blood Plasma Peptidome Analysis (2018)

The conditions for peptidome analysis of blood plasma were optimized and the efficacy of the proposed approach was compared with the methods described in the literature. The method implies solution of two main problems: inactivation of blood plasma proteases and dissociation of peptides from major blood plasma proteins, which they are quantitatively associated with. To solve these problems, we proposed a new method of sample preparation. The essence of the method is simultaneous denaturation of plasma proteins plus reduction and alkylation of thiol groups of Cys, which is achieved by heating a blood plasma sample (95°C) in the presence of sodium deoxycholate, tris(2-carboxyethyl)phosphine, and 2-chloroacetamide. After separation of peptides from proteins by ultrafiltration on microcentrifuge filters and removal of sodium deoxycholate, the peptides are identified by LC-MS/MS using a Q Exactive HF (Thermo Scientific) mass spectrometer. As a result of one LC-MS/MS run of the peptide mixture obtained from ~15 μL of blood plasma, 2257 peptide fragments of 867 proteins were identified, which is 1.5 times higher than the values achieved by using the generally accepted method of differential solubilization. Our immediate plans include the use of our approach for cataloguing human blood plasma peptides, as well as establishing the magnitude of individual variability and the features of the peptidome that are related to gender and age.