gebhart/patrepeval huggingface dataset:
Preventing Surgical Site Infections: A Surgeon's Perspective (2001)

Wound site infections are a major source of postoperative illness, accounting for approximately a quarter of all nosocomial infections. National studies have defined the patients at highest risk for infection in general and in many specific operative procedures. Advances in risk assessment comparison may involve use of the standardized infection ratio, procedure-specific risk factor collection, and logistic regression models. Adherence to recommendations in the 1999 Centers for Disease Control and Prevention guidelines should reduce the incidence of infection in surgical patients.
The relationship between antifungal diene levels and fungal inhibition during quiescent infection of unripe avocado fruits by Colletotrichum gloeosporioides (1991)

Quantitative changes in the antifungal compound, 1‐acetoxy‐2‐hydroxy‐4‐oxo‐heneicosa‐12.15‐diene, in freshly harvested avocado fruits during the initial stages of fungal development were investigated to determine the possible involvement of the compound in quiescent infections of Colletotrichum gloeosporioides. The concentration of the antifungal compound in the peel decreased to subfungitoxic concentrations 16 h after harvest. Fifty‐six hours later the antifungal diene had increased to c . 3800 μg/g fresh weight. At this stage, germinated appressoria had penetrated the cuticle to the epidermal cells but no fungal development was observed until 7 days later when the concentration of the diene had decreased to 100‐110μg/g fresh weight. Following a dip treatment at 55°C for 5 or 10 min, the antifungal diene concentration decreased as in the controls, but it remained at subfungitoxic concentrations for a longer period enabling fungal development and early symptom expression. The concentration of the diene in the flesh of freshly harvested fruit decreased to 120 μg/g fresh weight 24 h after harvest. Inoculation of peeled fruits with spores of C. gloeosporioides showed germination without appressoria formation and symptom expression occurred 24‐48 h later. Symptom expression was delayed if fruits were inoculated after coating the flesh with epicuticular wax extracts or if the flesh was inoculated 3 days after harvest when the antifungal diene had regained a fungitoxic concentration. Disease symptoms were expressed in soft fruits containing subfungitoxic concentrations of the diene. We conclude that the diene in unripe avocado fruits inhibits fungal development of germinated appressoria or conidia. The quiescent structure of C. gloeosporioides in unripe avocado fruit is a subcuticular hypha.
Progressive histogram reshaping for creative color transfer and tone reproduction (2010)

Image manipulation takes many forms. A powerful approach involves image adjustment by example. To make color edits more intuitive, the intelligent transfer of a user-specified target image's color palette can achieve a multitude of creative effects, provided the user is supplied with a small set of straightforward parameters. We present a novel histogram reshaping technique which allows significantly more control than previous methods. Given that the user is free to chose any image as the target, the process of steering the algorithm becomes artistic. Moreover, we show for the first time that creative tone reproduction can be achieved by matching a high dynamic range image against a low dynamic range target.
Activation of HIV Transcription by the Viral Tat Protein Requires a Demethylation Step Mediated by Lysine-specific Demethylase 1 (LSD1/KDM1) (2011)

The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications. Although individual modifications are well characterized, their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear.We examine interactions between two critical modifications within the RNA-binding domain of Tat: monomethylation of lysine 51 (K51) mediated by Set7/9/KMT7, an early event in the Tat transactivation cycle that strengthens the interaction of Tat with TAR RNA, and acetylation of lysine 50 (K50) mediated by p300/KAT3B, a later process that dissociates the complex formed by Tat, TAR RNA and the cyclin T1 subunit of the positive transcription elongation factor b (P-TEFb). We find K51 monomethylation inhibited in synthetic Tat peptides carrying an acetyl group at K50 while acetylation can occur in methylated peptides, albeit at a reduced rate. To examine whether Tat is subject to sequential monomethylation and acetylation in cells, we performed mass spectrometry on immunoprecipitated Tat proteins and generated new modification-specific Tat antibodies against monomethylated/acetylated Tat. No bimodified Tat protein was detected in cells pointing to a demethylation step during the Tat transactivation cycle. We identify lysine-specific demethylase 1 (LSD1/KDM1) as a Tat K51-specific demethylase, which is required for the activation of HIV transcription in latently infected T cells. LSD1/KDM1 and its cofactor CoREST associates with the HIV promoter in vivo and activate Tat transcriptional activity in a K51-dependent manner. In addition, small hairpin RNAs directed against LSD1/KDM1 or inhibition of its activity with the monoamine oxidase inhibitor phenelzine suppresses the activation of HIV transcription in latently infected T cells.Our data support the model that a LSD1/KDM1/CoREST complex, normally known as a transcriptional suppressor, acts as a novel activator of HIV transcription through demethylation of K51 in Tat. Small molecule inhibitors of LSD1/KDM1 show therapeutic promise by enforcing HIV latency in infected T cells.
FoxOs Function Synergistically to Promote Glucose Production (2010)

Hepatic glucose production (HGP) plays a vital role in maintaining the supply of glucose to the body, and transcription factor FoxO1 is known to confer hormone responsiveness onto HGP. Mice with a liver-specific FoxO1 deletion (L-FoxO1) show reduced HGP and reduced expression of glucose production genes. To determine the contribution of additional transcription factors to HGP, we created double and triple liver-specific knock-outs lacking FoxO1, FoxO3, and FoxO4 or the related protein FoxA2. We show that, when compared with single knock-out of FoxO1, triple ablation of FoxO genes causes more pronounced fasting hypoglycemia, increased glucose tolerance, and enhanced insulin sensitivity, with decreased plasma insulin levels. In contrast, combined ablation of FoxO1 and FoxA2 phenocopied the single knock-out of FoxO1. These data indicate that FoxOs work in concert to regulate multiple aspects of hepatic glucose metabolism.
Inactivation of Antibiotics and the Dissemination of Resistance Genes (1994)

The emergence of multidrug-resistant bacteria is a phenomenon of concern to the clinician and the pharmaceutical industry, as it is the major cause of failure in the treatment of infectious diseases. The most common mechanism of resistance in pathogenic bacteria to antibiotics of the aminoglycoside, beta-lactam (penicillins and cephalosporins), and chloramphenicol types involves the enzymic inactivation of the antibiotic by hydrolysis or by formation of inactive derivatives. Such resistance determinants most probably were acquired by pathogenic bacteria from a pool of resistance genes in other microbial genera, including antibiotic-producing organisms. The resistance gene sequences were subsequently integrated by site-specific recombination into several classes of naturally occurring gene expression cassettes (typically "integrons") and disseminated within the microbial population by a variety of gene transfer mechanisms. Although bacterial conjugation once was believed to be restricted in host range, it now appears that this mechanism of transfer permits genetic exchange between many different bacterial genera in nature.
Randomized phase II study of two schedules of flavopiridol given as timed sequential therapy with cytosine arabinoside and mitoxantrone for adults with newly diagnosed, poor-risk acute myelogenous leukemia (2012)

Both flavopiridol schedules produce comparably encouraging results in adults with poor-risk acute myelogenous leukemia. Given the greater ease of bolus administration, we are conducting a randomized phase II study of bolus flavopiridol followed by ara-c and mitoxantrone versus conventional induction therapy for patients aged 70 years and under with intermediate or poor-risk acute myelogenous leukemia. This study is registered at www.clinicaltrials.gov as #NCT 00407966.
Use of Vacuum-Assisted Closure for Healing of a Persistent Perineal Sinus Following Panproctocolectomy: Report of a Case (2004)

Perineal sinus is a troublesome complication after proctectomy for inflammatory bowel disease or rectal cancer. The results from treatment with simple dressings with or without surgical debridement are suboptimal. Definitive management may require complex operations with muscular or musculocutaneous flaps. Vacuum-assisted dressings have been used successfully for management of chronic wounds and soft tissue defects. This technique was successfully used in the management of a perineal sinus, which occurred after proctectomy for rectal cancer developing on a background of inflammatory bowel disease and preoperative radiotherapy.
Experimental validation of Monte Carlo modeling of fluorescence in tissues in the UV-visible spectrum (2003)

The goal of the work is to experimentally verify Monte Carlo modeling of fluorescence and diffuse reflectance measurements in turbid, tissue phantom models. In particular, two series of simulations and experiments, in which one optical parameter (absorption or scattering coefficient) is varied while the other is fixed, are carried out to assess the effect of the absorption coefficient (mu(a)) and scattering coefficient (mu(s)) on the fluorescence and diffuse reflectance measured from a turbid medium. Moreover, simulations and experiments are carried out for several fiber optic probe geometries that are designed to sample small tissue volumes. Additionally, a group of conversion expressions are derived to convert the optical properties and fluorescence quantum yield measured from tissue phantoms for use in Monte Carlo simulations. The conversions account for the differences between the definitions of the absorption coefficient and fluorescence quantum yield of fluorophores in a tissue phantom model and those in a Monte Carlo simulation. The results indicate that there is good agreement between the simulated and experimentally measured results in most cases. This dataset can serve as a systematic validation of Monte Carlo modeling of fluorescent light propagation in tissues. The simulations are carried out for a wide range of absorption and scattering coefficients as well as ratios of scattering coefficient to absorption coefficient, and thus would be applicable to tissue optical properties over a wide wavelength range (UV-visible/near infrared). The fiber optic probe geometries that are modeled in this study include those commonly used for measuring fluorescence from tissues in practice.
Detection of programmed cell death using fluorescence energy transfer (1998)

Fluorescence energy transfer (FRET) can be generated when green fluorescent protein (GFP) and blue fluorescent protein (BFP) are covalently linked together by a short peptide. Cleavage of this linkage by protease completely eliminates FRET effect. Caspase-3 (CPP32) is an important cellular protease activated during programmed cell death. An 18 amino acid peptide containing CPP32 recognition sequence, DEVD, was used to link GFP and BFP together. CPP32 activation can be monitored by FRET assay during the apoptosis process.
Th1-Biased Tertiary Lymphoid Tissue Supported by CXC Chemokine Ligand 13-Producing Stromal Network in Chronic Lesions of Autoimmune Gastritis (2003)

Secondary lymphoid tissue is developmentally programmed and characterized by well-ordered compartmentalization of lymphocyte subsets and specialized stromal cells supporting the tissue architecture. By contrast, tertiary lymphoid tissue is defined as that induced in ectopic sites by inflammation, although its immunological role is largely unknown. In this study, we characterize the lymphoid tissue induced in the chronic lesion of murine autoimmune gastritis (AIG). Within the lymphoid cluster in the gastric mucosa, there is a clear segregation of T and B cells. Follicle-like B cell areas are always located on the luminal side of the mucosa, while T cells are located in the basal part. A typical lymphoid reticular network and follicular dendritic cells support the structure. Importantly, complement receptor 1(+) follicular dendritic cells within the follicle express a B cell homing chemokine, CXC chemokine ligand 13. The number and size of the clusters correlate with the age of the mice and the serum autoantibody titer, suggesting the functional importance of the clusters in local Ab production, although involvement of the autoantibody in the disease progression is still unclear. AIG gastric lesions are known to constitute a Th1-biased, memory T cell-dependent immunomicroenvironment. The expression pattern of cytokines, including lymphotoxin-beta, and chemokines in the AIG stomach is consistent with this observation. Taken together, these facts suggest that, during the chronic phase of autoimmunity, long-lasting lymphocyte infiltration probably induces a unique tertiary lymphoid tissue that has a function distinct from that of regional lymph nodes. These neolymphoid tissues may maintain the local self reactivity supporting the vicious cycle of Th1-type reaction as well as autoantibody production.
Immunohistochemical evaluation of biological markers in mammary carcinoma in situ: correlation with morphological features and recently proposed schemes for histological classification (1996)

In situ carcinoma (CIS) of the breast, particularly of ductal type, is being diagnosed with increasing frequency owing to the widespread use of mammographic screening and there is considerable interest in the prognosis of different histological types of ductal carcinoma in situ (DCIS). Evaluation of biological markers as prognostic indicators in invasive breast carcinomas is well established. Antibodies to many of these markers are now available and immunohistochemical techniques can be applied to in situ as well as infiltrating carcinoma. Definite patterns of marker expression relating to both lobular carcinoma in situ (LCIS) and different morphological types of DCIS are now emerging. Poorly differentiated DCIS, usually of comedo pattern, tends to be oestrogen receptor (ER) and progesterone receptor (PR) negative, nearly always has a high proliferation rate and frequently expresses c-erbB-2 and p53 protein. LCIS and well differentiated DCIS, the latter usually of cribriform or micropapillary pattern, is nearly always ER and PR positive, has a low proliferation rate and rarely, if ever, expresses c-erbB-2 or p53 protein. Biological markers may help in both predicting the outcome of DCIS treated by conservation therapy and in establishing new criteria for histological classification.
Cutting Edge: CD4+CD25+ Alloantigen-Specific Immunoregulatory Cells That Can Prevent CD8+ T Cell-Mediated Graft Rejection: Implications for Anti-CD154 Immunotherapy (2002)

Blockade of CD40-CD154 interactions can facilitate long-term allograft acceptance in selected rodent and in primate models, but, due to the ability of CD154-independent CD8(+) T cells to initiate graft rejection, this strategy is not always effective. In this work we demonstrate that blockade of the CD40-CD154 pathway at the time of transplantation enables the generation of donor alloantigen-specific CD4(+)CD25(+) regulatory T cells, and that if the regulatory cells are present in sufficient numbers they can suppress allograft rejection mediated by CD154-independent CD8(+) T cells.
ChemInform Abstract: Telomerase Inhibitors — Oligonucleotide Phosphoramidates as Potential Therapeutic Agents (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Motion-planning chip speeds robots (2017)

If you've seen a robot manipulation demo, you've almost certainly noticed that the robot tends to spend a lot of time looking like it's not doing anything. It's tempting to say that the robot is “thinking” when this happens, and that might even be mostly correct: Odds are that you're waiting for some motion planning algorithm to figure out how to get the robot's arm and gripper to do what it's supposed to do without running into anything. This motion-planning process is one of the most important skills a robot can have, and it's also one of the most time consuming.
The insulin-like growth factor axis and prostate cancer: lessons from the transgenic adenocarcinoma of mouse prostate (TRAMP) model. (1999)

We have characterized the temporal expression of the insulin-like growth factor (IGF) axis in the transgenic adenocarcinoma of mouse prostate (TRAMP) model as prostate cancer progression in this model closely mimics that observed in the human disease, and the model provides samples representing the earliest stages of prostate cancer that are clinically the most difficult to obtain. We report that prostate-specific IGF-I mRNA expression increased during prostate cancer progression in TRAMP mice and was elevated in the accompanying metastatic lesions, whereas prostatic IGF-I mRNA remained at nontransgenic levels in androgen-independent disease. Expression of IGF-II mRNA, however, was reduced in primary prostate cancer, metastatic lesions, and androgen-independent disease. Expression of type-1 IGF receptor (IGF1R) mRNA, encoding the cognate receptor for both IGF-I and IGF-II, as well as type-2 IGF receptor (IGF2R) mRNA was not found to be altered during primary prostate cancer progression in intact TRAMP mice but was dramatically reduced in metastatic lesions and in androgen-independent disease. Similar to reports from clinical disease, serum IGF-I levels were observed to increase precociously in TRAMP mice early in disease progression but remained at nontransgenic levels after castration. Elevated serum levels of IGF-binding protein 2 were observed to correlate with advanced prostate cancer in the TRAMP model. Together these observations implicate IGF-I as an important factor during the initiation and progression of primary prostate cancer and provide evidence that there is a strong selection against expression of IGF1R and IGF2R in metastatic and androgen-independent disease.
Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy (2013)

The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Here, we developed a single-cell nanobiopsy platform based on scanning ion conductance microscopy (SICM) for continuous sampling of intracellular content from individual cells. The nanobiopsy platform uses electrowetting within a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. We demonstrate the subcellular resolution of the nanobiopsy platform by isolating small subpopulations of mitochondria from single living cells, and quantify mutant mitochondrial genomes in those single cells with high throughput sequencing technology. These findings may provide the foundation for dynamic subcellular genomic analysis.
Monitoring of Brain Spiking Activity and Autoantibodies to N‐Terminus Domain of GluR1 Subunit of AMPA Receptors in Blood Serum of Rats with Cobalt‐Induced Epilepsy (1998)

We have monitored EEG spontaneous spiking activity and analyzed serum from rats with cobalt-induced epilepsy for the presence of autoreactive antibodies to alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) glutamate receptor subunits. The presence and the level of autoantibodies were assessed using immunoblot and ELISA with synthetic peptide specific to the N-terminus domain of the GluR1 subunit of the AMPA receptor. Rats with cobalt-induced epilepsy exhibited strong GluR1 immunoreactivity at the end of the first week after surgery compared with vehicle-treated rats. We showed that GluR1 autoantibodies in blood serum of rats with cobalt-induced epilepsy preceded the spiking activity maximum in the EEG. Levels of autoantibodies to GluR1 detected in blood of these rats remained elevated when EEG spiking activity was significantly reduced and seizures disappeared. The EEG monitoring of spiking activity showed a correlation with accumulation of GluR1 autoantibodies in blood serum of rats with cobalt-induced epilepsy.
Metabolic and Functional Characterization of Human Adipose-Derived Stem Cells in Tissue Engineering (2008)

Adipose-derived stem cells are an excellent source of multipotent cells and are capable of advancing current tissue engineering methodologies. These data show that adipose-derived stem cells remain viable under adverse conditions of low glucose, glutamine, and oxygen concentrations. However, there are variable levels of differentiation in the various culture conditions, which could lead to challenges in de novo osteogenesis and other forms of tissue engineering. Therefore, these results should be used in developing specific strategies to ensure successful application of adipose-derived stem cells in bone engineering and similar applications.
Lower Airways Inflammation during Rhinovirus Colds in Normal and in Asthmatic Subjects (1995)

Abstract Human rhinoviruses (HRV) cause the majority of common colds and are etiologically linked with changes in lower airways physiology and asthma exacerbations. We hypothesized that changes in bronchial mucosal inflammatory cell populations may be responsible for HRV-induced changes in airway reactivity. We examined bronchial mucosal biopsies during experimental infections with HRV serotype 16 and measured changes in histamine reactivity. Seventeen adult volunteers (six atopic asthmatics) had baseline measurements of histamine reactivity and fiberoptic bronchoscopic biopsies, followed 2 wk later by viral inoculation. Further bronchial biopsies were taken on Day 4 of the infection and 6 to 10 wk later. Mast cells, eosinophils, lymphocytes, and neutrophils were quantified by immunohistochemical techniques. Infection was documented by viral culture, seroconversion, and symptoms. An increase in histamine responsiveness during the cold (p = 0.048) was accompanied by increases in submucosal lymphocytes (p = 0.050). There was a subsequent decrease in submucosal and epithelial lymphocytes in convalescence (p = 0.028; p = 0.030). There was an increase in epithelial eosinophils with the cold (p = 0.042), and in asthmatics this appeared to persist into convalescence. A peripheral blood lymphopenia correlated with increased responsiveness (r = 0.062, p = 0.014). Rhinoviral colds are associated with a bronchial mucosal lymphocytic and eosinophilic infiltrate that may be related to changes in airway responsiveness and asthma exacerbations.