gebhart/patrepeval huggingface dataset:
A quantitative evaluation of pigmented skin lesions using the L*a*b* color coordinates (2000)

The evaluation of pigmentary skin lesions by clinical doctors has been based on subjective and qualitative judgements. Observations have mostly relied on visual inspection, making the effects of treatment difficult to evaluate with any precision. For this reason there is a real need for an objective method to evaluate prognosis after treatment. Recent scientific measurements such as reflectance spectrophotometry and reflectance colorimetry have provided accurate quantitative color information about skin lesions, but these techniques are costly and difficult to apply in the clinical field. The purpose of this study was to develop a simple and cost-effective way of evaluating treatment results. We have developed a software program using the L*a*b* color coordinate system to quantify the effect of treatment and have successfully demonstrated its clinical usefulness. Our method compares the relative color difference between normal skin and skin lesions before and after treatment, instead of measuring the absolute color of skin lesions. The accuracy of our quantitative color analysis was confirmed by the simulated images of hemangioma and ota nevus. Clinical efficacy was also confirmed through a blind test involving 3 clinicians who were asked to grade the treatment effects of 13 cases of hemangioma and 7 cases of ota nevus. These subjective clinical grades correlated well with the treatment results obtained using the proposed color analysis system (Correlation coefficient = 0.84).
Effect of Reproductive History on Mammary Epithelial Biology (2001)

Epidemiologic studies have repeatedly demonstrated that women who undergo a first full-term pregnancy early in life have a significantly reduced lifetime risk of breast cancer. Similar to humans, rodents also display parity-induced protection against breast cancer. We have used high-density DNA oligonucleotide microarrays to identify genes whose expression in the murine mammary gland is persistently altered as a consequence of an early first full-term pregnancy. The panel of differentially expressed genes that we have isolated reproducibly distinguishes between the nulliparous and parous states of the mammary gland in multiple strains of mice and rats. We find that parity results in the persistent down-regulation of multiple genes encoding epithelial growth factors as well as the persistent up-regulation of growth-inhibitory pathways. Our studies further indicate that parity results in a persistent increase in the differentiated state of the mammary gland as well as persistent changes in the immunologic environment and hematopoietic cell types resident within the gland. These data provide the first molecular description of a developmental state of the mammary gland that is associated with reduced cancer risk and suggest novel hypotheses for the mechanistic basis by which parity may modulate breast cancer risk.
Exploring end user preferences for location obfuscation, location-based services, and the value of location (2010)

Long-term personal GPS data is useful for many UbiComp services such as traffic monitoring and environmental impact assessment. However, inference attacks on such traces can reveal private information including home addresses and schedules. We asked 32 participants from 12 households to collect 2 months of GPS data, and showed it to them in visualizations. We explored if they understood how their individual privacy concerns mapped onto 5 location obfuscation schemes (which they largely did), which obfuscation schemes they were most comfortable with (Mixing, Deleting data near home, and Randomizing), how they monetarily valued their location data, and if they consented to share their data publicly. 21/32 gave consent to publish their data, though most households' members shared at different levels, which indicates a lack of awareness of privacy interrelationships. Grounded in real decisions about real data, our findings highlight the potential for end-user involvement in obfuscation of their own location data.
Safety and efficacy of digital single-operator pancreatoscopy for obstructing pancreatic ductal stones (2019)

Abstract Background and study aims The role of the digital single-operator pancreatoscopy (D-SOP) with electrohydraulic (EHL) or laser lithotripsy (LL) in treating pancreatic ductal stones is unclear. We investigated the safety and efficacy of D-SOP with EHL or LL in patients with obstructing pancreatic duct stones. Patients and methods Retrospective analysis of 109 patients who underwent D-SOP for pancreatic stones at 17 tertiary centers in the United States and Europe from February 2015 to September 2017. Logistic regression was performed to identify factors associated with the need for more than one D-SOP with EHL/LL. Results Most patients were males (70.6 %),mean age 54.7 years. Fifty-nine (54.1 %) underwent EHL and 50 (45.9 %) underwent LL. Mean procedure time was longer in the EHL group (74.4 min vs 53.8 min; P &lt; 0.001). Ducts were completely cleared (technical success) in 89.9 % of patients (94.1 % in EHL vs 100 % in LL; P = 0.243), achieved in a single session in 73.5 % of patients (77.1 % by EHL and 70 % by LL; P= 0.5).D-SOP failed in 11 patients (10.1 %); 6 patients were treated with extracorporeal shockwave lithotripsy (ESWL), 1 with surgery,1 with combined treatment (ESWL + D-SOP EHL) and 3 with other. Fourteen adverse events occurred in 11 patients (10.1 %). Patients with more than three ductal stones were more likely to have technical failure compared to those with less than three stones (17 % vs. 4.8 %; P = 0.04). Having more than three stones was independently associated with the need for more than one D-SOC EHL/LL session (OR 2.94, 95 % CI 1.13 – 7.65). Conclusion D-SOP with EHL or LL is effective and safe in patients with pancreatic ductal stones.
An Efficient Resource to Accelerate Research into the Cause and Prevention of Breast Cancer: The Love/Avon Army of Women (2013)

Abstract Background: It is well established that more research into the cause and prevention of breast cancer is needed. While studies are done in cell lines and lab animals, translation of findings to women is often delayed due to difficulty in recruitment. The Dr. Susan Love Research Foundation received a grant from the Avon Foundation for Women to form the Love/Avon Army of Women (AOW); an on-line recruitment resource designed to partner women with researchers in order to accelerate breast cancer research. Methods: Researchers submit a proposal to the AOW Scientific Advisory Committee. If a study is accepted, a mass e-mail describing the study procedures and inclusion/exclusion criteria is sent to the entire AOW database. Women sign up at www.armyofwomen.org to join and receive AOW e-mails about breast cancer research studies. Women self-select based on interest and study criteria, and undergo a secondary on-line screening before contact information is passed on to the researcher for the enrollment process. Results: Over 371,000 women have signed up, including survivors and women without a history of breast cancer, ranging from ages 18 to 100, representing all 50 US states and 49 countries. To date, the AOW has recruited for 70 studies. The diversity of the AOW members has proved beneficial for many studies, such as those needing to enroll racial/ethnic minorities, women of varying sexual orientations, or young survivors. A secondary goal of the AOW is to assist researchers new to research with human subjects. The AOW has successfully helped researchers cross the chasm, coaching them on what it takes to transition their research from animal models to human subjects. Conclusions: The AOW has proved to be a successful resource for scientists to accelerate accrual, expand the number and diversity of their subject population and to obtain exactly the type of specimens they need when they need it. This partnership between women and scientists has revolutionized research and accelerated efforts to eradicate breast cancer. The public is ready and willing to partner with the research community to find the answer to urgent clinical problems.
Gelation‐Assisted Light Harvesting by Selective Energy Transfer from an Oligo(<i>p</i>‐phenylenevinylene)‐Based Self‐Assembly to an Organic Dye (2003)

Hot gels get turned off: Gelation of the title molecules facilitate transfer of excitation energy exclusively from the self-assembled nanostructures (see scheme path a) to Rhodamine B and not from the single molecules (path b), thereby establishing the role of self-assembled gel nanostructures in light harvesting. The emission from the dye can be shut off in a thermoreversible fashion since the self-assembly breaks to form molecular, dissolved oligo(phenylenevinylene)s above the gel melting temperature (Tgel).
Octahedral Coordination of an Iodide Ion in an Electrophilic Sandwich (2000)

An “anti-crown” sandwich: Symmetry-allowed interactions of the filled p orbitals of the iodide ion with the corresponding empty p orbitals of the mercury atoms of B-hexamethyl-9-mercuracarborand-3 result in three equivalent pHg-pI-pHg three-center, two-electron bonds (see picture) and a sandwich structure.
C-Terminal Zinc-Containing Peptide Required for RNA Recognition by a Class I tRNA Synthetase (1996)

Escherichia coli isoleucyl-tRNA synthetase is one of five closely related class I tRNA synthetases. The active site of the 939 amino acid polypeptide is in an N-terminal domain which contains an insertion believed essential for interactions with the tRNA acceptor helix. The enzyme was shown previously to contain an essential (for function in vivo) zinc bound to a Cys4 cluster at the C-terminal end of the polypeptide. The specific function of this zinc has been unknown. We show here that aminoacylation activity can be reconstituted in vitro by combining a 53 amino acid zinc-containing C-terminal peptide with a protein consisting of the remaining 886 amino acids. Reconstitution of aminoacylation is zinc-dependent. In contrast, the zinc-containing peptide is dispensable for synthesis of isoleucyl adenylate. Affinity coelectrophoresis showed that the 53 amino acid C-terminal peptide is required specifically for tRNA binding. We propose that the zinc-containing peptide curls back to the active site to make contact with the acceptor helix of bound tRNA, but not with isoleucine or ATP. It is the first example of a zinc-containing peptide in a class I tRNA synthetase that is essential for tRNA binding interactions. The design of this enzyme may be part of a more general scheme for class I tRNA synthetases to acquire acceptor helix binding elements during the development of the genetic code.
Plasma Levels of Vasoactive Intestinal Polypeptide and Oxytocin in Response to Suckling, Electrical Stimulation of the Mammary Nerve and Oxytocin Infusion in Rats (1990)

The aim of the present study was to measure plasma levels of vasoactive intestinal polypeptide (VIP) and oxytocin following suckling, electrical stimulation of the mammary nerve and oxytocin infusion in lactating rats. Trunk blood was collected by decapitation after 5 and 20 min of suckling in conscious lactating rats. Repeated blood samples were drawn from the carotid artery in anesthetized rats, in connection with suckling, oxytocin infusion (0.22 nmol/l/kg/h) and electrical stimulation of the mammary nerve (5 V, 5 Hz, 2 ms). VIP and oxytocin levels were measured by radioimmunoassay. In conscious rats, VIP levels rose significantly from 18 +/- 5 to 102 +/- 30 pM after 5 min of suckling and to 123 +/- 25 pM after 20 min of suckling when milk ejection occurred. Oxytocin levels rose significantly from 90 +/- 24 to 269 +/- 45 pM during milk ejection. Suckling, oxytocin infusion and mammary nerve stimulation in anesthetized rats raised VIP levels significantly from 13 +/- 2, 18 +/- 5 and 10 +/- 2 to 43 +/- 8, 45 +/- 16 and 53 +/- 22 pM, respectively, whereas oxytocin levels rose from 111 +/- 34 to 294 +/- 66 pM after 20 min of suckling and to a peak value of 500 +/- 70 pM after oxytocin infusion. This study shows that VIP is elevated in plasma in lactating rats when the pups are suckling. The results showing that VIP levels rise following mammary nerve stimulation and oxytocin infusions indicate that both neurogenic and hormonal mechanisms can contribute to the regulation of VIP levels in plasma.
Decline in NRF2‐Regulated Antioxidant Pathway in Advanced COPD Patient Lungs Due to DJ‐1 Deficit (2008)

NRF2, a bZIP transcription factor regulates a battery of cytoprotective genes and protects mice from cigarette smoke‐induced emphysema by attenuating oxidative stress and inflammation. However, NRF2's role in human COPD is unknown. Here, we analyzed expression of NRF2 and its transcriptional targets in non‐emphysematous (NE) lungs, mild COPD lungs (GOLD 1‐2), and advanced COPD lungs (GOLD 3‐4). NRF2‐mediated transcriptional targets (NQO1, HO‐1 and GCLM) declined in advanced COPD, even though there was greater oxidative stress, as evident from increased lipid peroxidation and decreased GSH levels. NRF2 protein but not NRF2 mRNA was dramatically reduced in advanced COPD lungs. KEAP1 protein, the cytoplasmic inhibitor of NRF2, showed no significant difference between NE and COPD lungs. Conversely, DJ‐1, which stabilizes NRF2, showed a significant decrease in both mRNA and protein expression in advanced COPD lungs. Knockdown of DJ‐1 in human lung epithelial (Beas2B) cells and mouse lungs by siRNA significantly decreased Nrf2 protein expression and attenuated induction of antioxidants in response to cigarette smoke exposure. Taken together, in advanced COPD patient lungs, there is a significant decline in Nrf2 protein stability that results in decreased antioxidant protection and increased oxidative stress. Decline in the NRF2 pathway may play an important role in the pathological progression of COPD.
1040-P: Survival Models of Diabetes Complications Applied to Different Cohorts (2021)

Background: EMRs have enabled the application of machine learning (ML) to characterize disease progression. ML requires large data to produce meaningful results, thus penalizing health systems with small EMRs. Applying models pre-trained on different EMRs is useful but may also suffer from discrepancies between medical sites using different disease codes, procedures, etc. We study the models trained on a large EMR and applied on a smaller one to estimate T2DM complication time using survival models.Method: We trained survival models on a large US insurance claim dataset to create a right-censored cohort (C_1) that includes onset time of T2DM complications, patient profiles, and disease histories. We constructed features using age, sex, and past occurrences of 250 most frequent Clinical Classification Software codes. We trained Random Survival Forest (RSF) models on this cohort. We then created another cohort (C_2) from a smaller EMR from a large Japanese hospital, on which we trained RSF models and also applied models trained on C_1.Results: Table 1 shows a feature importance ranking of trained RSF models and C-indices results. When applying C_1 pre-trained models to C_2, C-indices are high in Nephrology, Hyperosmolar, and Neuropathy. In these cases, common features are highly ranked by both models.Conclusions: This study illustrates the applicability of survival models with disease code covariates on cohorts from different geos.View largeDownload slideView largeDownload slide DisclosureA. Koseki: Employee; Self; IBM, Research Support; Self; Astellas Pharma Inc. M. Makino: None. A. Suzuki: Research Support; Self; Chugai Pharmaceutical Co., Ltd., Ono Pharmaceutical Co., Ltd., Taisho Pharmaceutical Co., Ltd., Takeda Pharmaceutical Co., Speaker’s Bureau; Self; Eli Lilly Japan K. K. R. Tokumasu: None. P. Chakraborty: None. M. Ghalwash: None. T. Iwamori: None. M. Kudo: Employee; Self; IBM. D. Sow: None. H. Yanagisawa: None. R. Yanagiya: None.
Proton magnetic resonance spectroscopic imaging of human breast cancer: A preliminary study (2003)

MRSI measurements of Cho are feasible in the human breast, and the SNR for Cho was significantly different between benign and malignant lesions. The potential advantages of MRSI over SV spectroscopy include the ability to assess multiple lesions as well as tissue with normal MRI appearance, as well as to perhaps gauge lesion borders and infiltration into surrounding tissue.
Volume quantification by contrast-enhanced ultrasound and thermodilution: an in vitro comparison (2013)

In clinical practice, blood volumes (BV) are typically measured by thermodilution. Recently, contrast-enhanced ultrasound (CEUS) has been proposed as an alternative minimally invasive approach for BV assessment [1]. This method measures BV using a single peripheral injection of a small bolus of ultrasound contrast agent (UCA) detected by an ultrasound scanner. By measuring the acoustic backscatter, two indicator dilution curves (IDCs) can be derived from two different sites in the circulatory system. IDC analysis permits deriving the mean transit time (MTT) the bolus takes to travel between the injection site and two measurement sites. Assessment of the BV between these sites is obtained by multiplying the difference in MTT (ΔMTT) by the blood flow. In this study, we compare different volumes in an in vitro set-up by CEUS with true set-up volumes and thermodilution acquired volumes.
1‐Aminoindan‐1,5‐dicarboxylic acid and (S)‐(+)‐2‐(3′‐carboxybicyclo[1.1.1] pentyl)‐glycine, two mGlu1 receptor‐preferring antagonists, reduce neuronal death in in vitro and in vivo models of cerebral ischaemia (1999)

Metabotropic glutamate (mGlu) receptors have been implicated in a number of physiological and pathological responses to glutamate, but the exact role of group I mGlu receptors in causing postischaemic injury is not yet clear. In this study, we examined whether the recently-characterized and relatively selective mGlu1 receptor antagonists 1-aminoindan-1,5-dicarboxylic acid (AIDA) and (S)-(+)-2-(3'-carboxybicyclo[1.1.1]pentyl)-glycine (CBPG) could reduce neuronal death in vitro, following oxygen-glucose deprivation (OGD) in murine cortical cell and rat organotypic hippocampal cultures, and in vivo, after global ischaemia in gerbils. When present in the incubation medium during the OGD insult and the subsequent 24 h recovery period, AIDA and CBPG significantly reduced neuronal death in vitro. The extent of protection was similar to that observed with the nonselective mGlu receptor antagonist (+)-alpha-methyl-4-carboxyphenylglycine [(+)MCPG] and with typical ionotropic glutamate (iGlu) receptor antagonists. Neuroprotection was also observed when AIDA or CBPG were added only after the OGD insult was terminated. Neuronal injury was not attenuated by the inactive isomer (-)MCPG, but was significantly enhanced by the nonselective mGlu receptor agonist (1S,3R)-1-aminocyclopentane-1, 3-dicarboxylic acid [(1S,3R)-ACPD] and the group I mGlu receptor agonist 3,5-dihydroxyphenylglycine (3,5-DHPG). The antagonists (+)MCPG, AIDA and CBPG were also neuroprotective in vivo, because i. c.v. administration reduced CA1 pyramidal cell degeneration examined 7 days following transient carotid occlusion in gerbils. Our results point to a role of mGlu1 receptors in the pathological mechanisms responsible for postischaemic neuronal death and propose a new target for neuroprotection.
Periplasmic Expression of Antibody Fragments (2014)

This chapter focuses on the biology and practical techniques that can help in the expression of antibody fragments in E. coli. The periplasm is often preferred for expression of soluble antibody fragments and some of the factors for this choice are discussed. The periplasm is the site of expression for only ~1/10 of the soluble proteins of E. coli and does not contain any DNA or RNA that can interfere with purification. Therefore combination of periplasmic expression with carefully considered harvest and extraction regimes can result in a very useful concentration and partial purification/enrichment of the periplasmic protein of interest. An important factor for enabling useful levels of protein expression is good selection or design of the expression plasmid. The key areas considered here are: (i) plasmid copy number/origin of replication, (ii) constitutive versus inducible promoter, (iii) resistance/selection marker, and (iv) design of the coding region. The phoA promoter along with depletion of phosphate has also been used to good effect for the production of antibody fragments. A notional advantage of periplasmic expression over extracellular expression is the ability to concentrate the product simply by harvesting the cells by centrifugation or filtration and avoiding vortex-type protein damage. The chapter describes various designs of antibody fragments along with the engineered adaptations and improvements to both the fragment and the host. The endoplasmic reticulum of eukaryotes is the natural site for the folding and assembly of antibodies.
Nanoscale elastic imaging: a new metrology tool for low-k dielectric integration (2002)

A new characterization tool based on ultrasonic force microscopy (UFM) has been developed to image the nanoscale mechanical properties of metal/low-k polymer damascence test structures. Metal and polymer regions are differentiated on the basis of elastic modulus with a spatial resolution /spl les/10 nm. This technique reveals a RIE-induced hardening of the low-k polymer at the metal/polymer interface and offers new opportunities for metrological reliability evaluation of low-k integration processes.
Stratifying High Dimensional Data Based on Proximity to the Convex Hull Boundary (2016)

The convex hull of a set of points, $C$, serves to expose extremal properties of $C$ and can help identify elements in $C$ of high interest. For many problems, particularly in the presence of noise, the true vertex set (and facets) may be difficult to determine. One solution is to expand the list of high interest candidates to points lying near the boundary of the convex hull. We propose a quadratic program for the purpose of stratifying points in a data cloud based on proximity to the boundary of the convex hull. For each data point, a quadratic program is solved to determine an associated weight vector. We show that the weight vector encodes geometric information concerning the point's relationship to the boundary of the convex hull. The computation of the weight vectors can be carried out in parallel, and for a fixed number of points and fixed neighborhood size, the overall computational complexity of the algorithm grows linearly with dimension. As a consequence, meaningful computations can be completed on reasonably large, high dimensional data sets.
Statistical Shape Models for Object Recognition and Part Localization (2006)

This paper deals with part-based object recognition. We present a statistical shape model that characterizes both variations intrinsic to an object class and perturbations unique to each observation. Object parts, constrained by the learned shape model, are efficiently localized using the max-product algorithm on a triangulated Markov random field (TMRF). As a combination of both techniques, our system is able to recognize objects with large deformations and locate their parts accurately. We test our method on standard databases. The recognition performance is compared to the state of the art and favorable results are reported.