gebhart/patrepeval huggingface dataset:
Population-based Case-Control Study of Diabetes and Breast Cancer Risk in Hispanic and Non-Hispanic White Women Living in US Southwestern States (2007)

Diabetes mellitus has been associated with breast cancer, although no studies appear to have adequately assessed the association in Hispanic women, a population with a high prevalence of diabetes. The authors investigated this association in a population-based case-control study of Hispanic and non-Hispanic White women living in the southwestern United States. Breast cancer cases diagnosed in 1999-2004 were identified through state cancer registries (1,526 non-Hispanic Whites, 798 Hispanics). Age- and ethnicity-matched controls (1,599 non-Hispanic Whites, 924 Hispanics) were selected from commercial mailing lists and driver's license and Social Security records. Diabetes history was assessed through interviewer-administered questionnaires. Odds ratios and 95% confidence intervals were calculated using logistic regression, adjusting for age, body mass index at age 15 years, and parity. Having any type of diabetes was not associated with breast cancer overall (odds ratio = 0.94, 95% confidence interval: 0.78, 1.12). Type 2 diabetes was observed among 19% of Hispanics and 9% of non-Hispanic Whites but was not associated with breast cancer in either group. Gestational diabetes was inversely associated with breast cancer in both ethnic groups, especially when first diagnosed at age < or =35 years (odds ratio = 0.54, 95% confidence interval: 0.37, 0.79). In this study, diabetes was not associated with breast cancer overall, although the inverse association with gestational diabetes warrants further investigation.
Polyphosphates and poly-β-hydroxybutyrate granules identification through quantitative image analysis in enhanced biological phosphorus removal systems (2011)

Enhanced biological phosphorus removal (EBPR) is a widely implemented technique for having the potential to cheaply and reliably remove phosphate from wastewater treatment processes, than traditional chemical methods. EBPR is performed by operating the system sequentially with anaerobic and aerobic conditions. Several studies were already performed ranging from different strategies for the competition between polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) to modeling both types of bacterial activities. Until now, slight attention has been given to the development of newer, faster, simpler, and better suited monitoring techniques for this type of system. This work is focused on the development of image analysis techniques for polyphosphates and poly-β-hydroxybutyrate granules in EBPR systems since off-line analyses are labor intensive and not able to be performed in full-scale plants. A lab-scale sequencing batch reactor fed with synthetic wastewater containing volatile fatty acids (VFAs) and orthophosphate was used. The reactor had a working volume of 4 L and was operated with a cycle time of 6 h consisting of 2 h anaerobic, 3 h aerobic, 50 min settling and decanting, and 5 min anaerobic idle periods. In each cycle, 2 L of synthetic wastewater was fed to the reactor in the ﬁrst 5 min of the anaerobic period, resulting in a hydraulic retention time (HRT) of 12 h. The pH was controlled during both the anaerobic and aerobic periods around 7, and the temperature was controlled at 30 ºC in order to provide selective advantages to GAOs over PAOs. The ratio between chemical oxygen demand (COD) and P in the feed was kept at 10 (gCOD/g P). Biomass samples were collected at the end of the anaerobic and aerobic phases and fixed with phosphate buffer saline solution (PBS) and ethanol. Two fluorescence staining methods were used: (1) DAPI for poly-P identification; and (2) nile blue for poly-β-hydroxybutyrate granules. So far, promising results were achieved regarding the type of images achieved by these fluorescence staining methods and the image analysis procedures still under development.
Functional MRI in Conjunction with a Novel MRI-compatible Hand-induced Robotic Device to Evaluate Rehabilitation of Individuals Recovering from Hand Grip Deficits (2019)

Functional magnetic resonance imaging (fMRI) is a non-invasive magnetic resonance imaging technique that images brain activation in vivo, using endogenous deoxyhemoglobin as an endogenous contrast agent to detect changes in blood-level-dependent oxygenation (BOLD effect). We combined fMRI with a novel robotic device (MR-compatible hand-induced robotic device [MR_CHIROD]) so that a person in the scanner can execute a controlled motor task, hand-squeezing, which is a very important hand movement to study in neurological motor disease. We employed parallel imaging (generalized auto-calibrating partially parallel acquisitions [GRAPPA]), which allowed higher spatial resolution resulting in increased sensitivity to BOLD. The combination of fMRI with the hand-induced robotic device allowed precise control and monitoring of the task that was executed while a participant was in the scanner; this may prove to be of utility in rehabilitation of hand motor function in patients recovering from neurological deficits (e.g., stroke). Here we outline the protocol for using the current prototype of the MR_CHIROD during an fMRI scan.
Crosslinking of thermoplastic composites using electron beam radiation (1991)

The crosslinking of thermoset materials has been clearly demonstrated to improve many desirable physical and chemical properties for composite applications. While thermoplastic resins also offer many advantages for composite applications, they are not crosslinked and, therefore, may not meet the same property criteria as crosslinked thermosets. Electron beams have been used successfully for crosslinking non-reinforced thermoplastic materials. Electron beams have also been used for curing composite thermoset materials. This research utilizes electron beams to crosslink high performance thermoplastic composite materials (PEEK and PPS with glass and carbon fibers). The tensile strength and tensile modulus are compared under various crosslinking conditions. The method is found to have some advantages in potentially improving physical properties of thermoplastic composite materials.
Computer assisted laparoscopic pneumovesical ureter reimplantation a.m. Cohen: initial experience in a pig model. (2003)

To assess the feasibility of a new variant of laparoscopic Cohen cross-trigonal ureter reimplantation in vesico-ureteral reflux (VUR) using telesurgical equipment. VUR was induced in 8 female pigs by transurethral unroofing of the ureteric orifices. Three months later the reflux was verified by a cystography. A cross-trigonal ureter reimplantation a.m. Cohen was performed by laparoscopic access to the bladder using the da Vinci telesurgical system. The 12 mm camera port was placed below the umbilicus, two 8 mm working ports for the robotic system were placed lateral to the rectus muscles and an additional port for assistance between camera and right working port. The outcome was assessed 3 months later by a new cystography. The operative time for a single reimplantation varied from 45 to 90 minutes. In all pigs the reflux disappeared after the procedure, which was complicated by a postoperative port hernia in two animals. Laparoscopic transvesical ureter reimplantation using telesurgical equipment is a feasible method in the few cases this procedure is indicated. The advantage of the robotic equipment is the better access to submucosal tunneling of the ureter and the intravesical suturing of the anastomosis indicated by shorter operative time and success rates similar to the open procedure.
pH‐induced structural transitions of bovine serum albumin (1993)

1. Titration curves have been constructed for all the resolvable resonances of defatted bovine serum albumin [pH meter readings in 2H2O solution (pH*) 2-10], including complete curves for six His residues and partial curves for a further four. Three His residues have unusually low pKa values (less than 5.5). 2. Abrupt discontinuities in the titration curves of nearly all resonances were observed near pH 4.3 (N to F transition), together with a marked loss of chemical shift dispersion at low pH*. No such loss of dispersion occurs in the high pH region previously associated with the N to B transition (approximately pH 8). The NMR data provide strong evidence that the N to F transition is not localised in domain III as had been previously suggested. 3. A localised unfolding of the N-terminal region occurs below pH* 4.5.
Near-Duplicate Video Detection Using Temporal Patterns of Semantic Concepts (2009)

Methods for video copy detection are typically based on the use of low-level visual features. However, low-level features may vary significantly for near-duplicates, which are video sequences that have been the subject of spatial or temporal modifications. As such, the use of low-level visual features may be inadequate for detecting near-duplicates. In this paper, we present a new video copy detection method that aims to identify near-duplicates for a given query video sequence. More specifically, the proposed method is based on identifying semantic concepts along the temporal axis of a particular video sequence, resulting in the construction of a so-called semantic video signature. The semantic video signature is then used for the purpose of similarity measurement. The main advantage of the proposed method lies in the fact that the presence of semantic concepts is highly robust to spatial and temporal video transformations. Our experimental results show that the use of a semantic video signature allows for the efficient and effective detection of near-duplicates.
Characterization of Prepreg Tack for Composite Manufacturing by Automated Fiber Placement (2019)

Automated fiber placement (AFP) has become the industry standard for large-scale production of carbon fiber reinforced plastics (CFRP) to improve rate and reduce defects associated with manual layup. Still, defects generated during AFP processes require manual, painstaking inspection by technicians and rework of the part when substantial defects are found. Prepreg (carbon fiber infused with uncured epoxy resin) tack is one of the primary factors that influences the generation of defects that arise during auto-mated fiber placement (AFP). Tack, as it relates to AFP processes and defect formation, can be understood as a combination of two stages, cohesion and decohesion. During the cohesion phase, two pieces of prepreg are brought into contact under elevated temperature and pressure. Compaction of the resin within the contact area will result in a degree of intimate contact, I, between the mating prepreg surfaces. Defect formation, as a result of decohesion between prepreg surfaces, occurs after the cohesion phase and arises due to stress from events such as fiber placement over an existing defect, on a contoured path, etc. (Figure 1). Tack strength resists the displacement of prepreg on a surface due to stresses developed during deposition.
NTOX-12. OBESITY AS A POTENTIAL ATTRIBUTE FOR VINCRISTINE INDUCED PERIPHERAL NEUROPATHY (2017)

Leukemia is the most common pediatric cancer (ages 0-19; 26% of pediatric cancers) with acute lymphoblastic leukemia (ALL) being the most common subtype (75%). Due to improved multidrug treatment regimens over the past 40 years, the 5-year survival rate for these children has increased from 57% to 90%. Vincristine is a core chemotherapeutic agent in the standard multidrug treatment plan. However, due to vincristine exposure, approximately 78% of these children will develop peripheral neuropathy (Vincristine-induced peripheral neuropathy: VIPN), which may be severe in some patients. The development of VIPN is characterized by progressive motor, sensory and autonomic loss of function and usually results in dose reductions of vincristine during treatment and thus an overall loss of therapeutic efficacy. Thus it is important to understand which children may be more vulnerable to developing VIPN. We hypothesized that ALL patients who were characterized as obese at time of diagnosis would develop worse neuropathy than ALL patients who were of healthy weight. Pediatric patients between the ages of two and eighteen diagnosed with pre B-cell ALL and receiving vincristine as part of their primary chemotherapy treatment plan were enrolled prior to day 8 of initiating vincristine. Neuropathy exams were performed prospectively to assess each patient’s VIPN using The Total Neuropathy Score (TNS). Weight categories were assigned to each patient based on his/her BMI percentile. An unpaired t test was done to evaluate the difference in maximum TNS-5 item score between obese and healthy patients. We found that obese pediatric ALL patients had a significantly higher maximum TNS score than pediatric ALL patients of healthy weights (p= 0.03). Future studies investigating healthy and obese ALL patients’ recovery times from VIPN are needed to assess obesity as a risk factor not only for severity of VIPN but also chronicity of this life-altering toxicity.
Changes in RNFL Thickness According to the Myopia in Patients with Glaucoma and Ocular Hypertension (2008)

Purpose: To evaluate the changes in retinal nerve fiber layer (RNFL) thickness according to the degree of myopia in patients with glaucoma and ocular hypertension. Methods: Ninety-eight patients (165 eyes) diagnosed with glaucoma or ocular hypertension underwent optical coherence tomography (OCT) and scanning laser polarimetry using variable corneal compensation (GDx-VCC) to analyze the correlation between the degree of myopia and the thickness of the RNFL. A partial correlation coefficient analysis was performed to adjust for various factors such as age, laterality, intraocular pressure, and the mean deviation from visual field test, which can influence the RNFL thickness. Results: The average, nasal, superior, and inferior sectorial RNFL thicknesses measured by OCT significantly decreased with increasing myopia (p
Supplementary Tables 1-2 from Breast Cancer Index Identifies Early-Stage Estrogen Receptor–Positive Breast Cancer Patients at Risk for Early- and Late-Distant Recurrence (2023)

&lt;p&gt;Supplementary Tables 1-2 - PDF file 101K, Supplementary Table 1. Kaplan-Meier estimates of overall distant recurrence free survival (DRFS) for 3 BCI risk groups in Stockholm TAM-treated and Multi-institutional cohorts. Supplementary Table 2. Overall distant recurrence: Univariate and multivariate Cox model analysis after stepwise variable selection by AIC of likelihood of overall distant recurrence in Stockholm TAM and Multi-institutional cohorts for all ER+ and ER+, HER2- patients&lt;/p&gt;
Abstract 1000: Rad6B induced β-catenin stabilization requires intact Wnt signaling (2010)

Abstract Aberrant activation of Wnt signaling results from stabilization and transcriptional activation of β-catenin and is often associated with carcinogenesis. Clinical evidence suggests that β-catenin accumulation occurs in breast cancer although activating mutations are rare. We have previously shown that Rad6B positively regulates β-catenin stability and transcriptional activity in breast cancer cells by inducing stable polyubiquitin modifications. Here we show that Rad6B physically interacts with β-catenin within the β-catenin amino acid segment containing the first armadillo repeat, which is also a binding site for casein kinase 1 (CK1). β-catenin phosphorylation by GSK3β and subsequent ubiquitination and proteasomal degradation is dependent upon CK1-mediated initiating phosphorylation of β-catenin at Ser45. In vitro kinase assays showed that Rad6B inhibits Ser45 phosphorylation by CK1, and Ser45 phosphorylated β-catenin is decreased in Rad6B overexpressing breast cancer cells. In vitro and in vivo mapping, and site-directed mutation analysis identified K394 of β-catenin as the predominant site for ubiquitination by Rad6B. MCF-7 breast cancer cells engineered to express myc-tagged K394R-β-catenin showed decreased steady-state levels and β-catenin transcriptional activity as compared to cells expressing wild type β-catenin. We also determined whether Rad6B-mediated β-catenin stabilization occurs independently of the canonical Wnt signaling pathway. MDA-MB-231 breast cancer cells overexpressing endogenous Rad6B were isolated on the basis of Rad6B promoter activity, and the consequences of Wnt disruption on β-catenin levels, transcriptional activity and Rad6B expression were determined by expressing a dominant negative mutant of Wnt coreceptor, LRP6. Disruption of Wnt signaling inhibited Rad6B expression and β-catenin accumulation. Both Wnt signaling disruption and Rad6B silencing separately enhanced localization of β-catenin on the cell membranes and decreased intracellular β-catenin accumulation. In summary, our data suggest that the Rad6B overexpression frequently observed in breast carcinomas contribute to β-catenin stabilization and transcriptional activation by inhibiting the CK1-mediated initiating phosphorylation and by ubiquitinating K394. However, the Rad6B induced β-catenin stabilization requires intact Wnt signaling. Supported by DOD W81XWH07-1-0562. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1000.
Studies of human polyclonal and monoclonal antibodies binding to lupus autoantigens and cross-reactive antigens (2003)

Human anti-DNA reactivity includes the same fine specificity as that present in murine anti-DNA reactivity. Peptide binding might be a useful surrogate marker for SLE.
A Role for B Cell-Activating Factor of the TNF Family in Chemically Induced Autoimmunity (2005)

After exposure to subtoxic doses of heavy metals such as mercury, H-2s mice develop an autoimmune syndrome consisting of the rapid production of IgG autoantibodies that are highly specific for nucleolar autoantigens and a polyclonal increase in serum IgG1 and IgE. In this study, we observe that HgCl2 administration in susceptible mice results in the elevated production of B cell-activating factor of the TNF family ((BAFF) also known as BLyS, TALL-1, zTNF-4, THANK, and TNSF13B), a B cell growth factor belonging to the TNF family. A transmembrane activator and calcium-modulating and cyclophilin ligand interactor (TACI)-Ig fusion protein (which neutralizes both BAFF and a proliferation-inducing ligand (APRIL), another TNF family member) inhibited Hg-induced autoantibody or serum IgE production. These results are discussed in the context of the inhibitory effect of TACI-Ig on B cell maturation at the transitional stage.
Throughput Modeling of Large-Scale 802.11 Networks (2008)

The success of dynamic spectrum access through simple listen-before-talk etiquettes has made way for opening up the spectrum. However, many problems still remain in this kind of networks. Stations might not be able to sense as much transmissions and hence defer channel access less often than their neighbors. This can lead to unfairness or (worst-case) starvation of certain terminals. In this paper we model the throughput of a large-scale 802.11 network. Although the fairness issues in these networks are known, network modeling is still focusing on small-scale rigid networks. We want to open up this research toward large-scale randomly distributed topologies. A new model is developed to predict the long-term throughput of flows inside such a large-scale 802.11 network. Our model is validated through ns-2 simulations.
Bioinspired Design of Artificial Signaling Systems (2022)

Natural systems use weak interactions and avidity effects to give biological systems high specificity and signal-to-noise ratios. Here we describe design principles for engineering fusion proteins that target therapeutic fusion proteins to membrane-bound signaling receptors by first binding to designer-chosen co-receptors on the same cell surface. The key design elements are separate protein modules, one that has no signaling activity and binds to a cell surface receptor with high affinity and a second that binds to a receptor with low or moderate affinity and carries out a desired signaling or inhibitory activity. These principles are inspired by natural cytokines such as CNTF, IL-2, and IL-4 that bind strongly to nonsignaling receptors and then signal through low-affinity receptors. Such designs take advantage of the fact that when a protein is anchored to a cell membrane, its local concentration is extremely high with respect to those of other membrane proteins, so a second-step, low-affinity binding event is favored. Protein engineers have used these principles to design treatments for cancer, anemia, hypoxia, and HIV infection.
Supplementary Tabes 1, 3 and 4 from Cytoplasmic Cyclin E Predicts Recurrence in Patients with Breast Cancer (2023)

&lt;p&gt;The attached files include 3 supplemental tables&lt;/p&gt;
10.2172/1239281 (2016)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Modeling file-sharing with BitTorrent-like incentives (2007)

We propose a new model for file-sharing peer-to-peer (P2P) networks that mimics the incentives provided by the popular BitTorrent system. In it, larger files are split into chunks and a peer can download or swap only one chunk at a time. We propose a Markov chain model in continuous time that resembles a stochastic epidemic/coagulation model. We prove that the Markov chain is approximated by a differential equation which, by itself, can give some rough information about the performance of the system. Finally, using this model, we explore the performance of BitTorrent-like incentives for an open system with peer departures and arrivals and a single file (torrent) with two chunks.
SAR-Processing-Algorithms. (1996)

!bersichtsvortrag ber die Prozessierungsaktivitten am Institut fr Hochfrequenztechnik der DLR. Vorstellung neuer Prozessierungsalgorithmen basierend auf dem Chirp-Scaling- Verfahren, dem SPECAN-Verfahren, neuen Datenreduktionsverfahren.
Increased Brain Gray Matter in the Primary Somatosensory Cortex is Associated with Increased Pain and Mood Disturbance in Patients with Interstitial Cystitis/Painful Bladder Syndrome (2014)

These data support the notion that changes in somatosensory gray matter may have an important role in pain sensitivity as well as affective and sensory aspects of interstitial cystitis. Further studies are needed to confirm the generalizability of these findings to other pain conditions.