gebhart/patrepeval huggingface dataset:
Oral biofilms: a reservoir of transferable, bacterial, antimicrobial resistance (2010)

Oral microbes are responsible for dental caries and periodontal diseases and have also been implicated in a range of other diseases beyond the oral cavity. These bacteria live primarily as complex, polymicrobial biofilms commonly called dental plaque. Cells growing within a biofilm often exhibit altered phenotypes, such as increased antibiotic resistance. The stable structural properties and close proximity of the bacterial cells within the biofilm appears to be an excellent environment for horizontal gene transfer, which can lead to the spread of antibiotic resistance genes amongst the biofilm inhabitants. This article will present an overview of the different types and amount of resistance to antibiotics that have been found in the human oral microbiota and will discuss the oral inhabitants’ role as a reservoir of antimicrobial resistance genes. In addition, data on the genetic support for these resistance genes will be detailed and the evidence for horizontal gene transfer reviewed, demonstrating that the bacteria inhabiting the oral cavity are a reservoir of transferable antibiotic resistance
Void detection in copper interconnects using energy dispersive x-ray spectroscopy (2012)

The formation of small voids in narrow sub-50 nm Cu interconnect lines during their fabrication is a major challenge for the development of integrated circuits. Focused ion beam sectioning and scanning electron microscopy imaging are being used for void detection during process development, but as they are destructive, they are less suited for in-line metrology. Therefore, the authors developed a nondestructive method based on energy dispersive x-ray spectroscopy where voids can be detected as changes in x-ray intensity due to the direct proportionality of the generated characteristic x-ray intensity with the amount of copper atoms contained in the interaction volume. The procedure allows the detection of small voids down to 15 nm in a fast and nondestructive way. This is possible for thin and chemically mechanically polished Cu interconnects where intensity variations due to thickness variations can be ignored.
Combination of Prostate-Specific Antigen, Clinical Stage, and Gleason Score to Predict Pathological Stage of Localized Prostate Cancer (1997)

<h3>Objective.</h3> —To combine the clinical data from 3 academic institutions that serve as centers of excellence for the surgical treatment of clinically localized prostate cancer and develop a multi-institutional model combining serum prostate-specific antigen (PSA) level, clinical stage, and Gleason score to predict pathological stage for men with clinically localized prostate cancer. <h3>Design.</h3> —In this update, we have combined clinical and pathological data for a group of 4133 men treated by several surgeons from 3 major academic urologic centers within the United States. Multinomial log-linear regression was performed for the simultaneous prediction of organ-confined disease, isolated capsular penetration, seminal vesicle involvement, or pelvic lymph node involvement. Bootstrap estimates of the predicted probabilities were used to develop nomograms to predict pathological stage. Additional bootstrap analyses were then obtained to validate the performance of the nomograms. <h3>Patients and Settings.</h3> —A total of 4133 men who had undergone radical retropubic prostatectomy for clinically localized prostate cancer at The Johns Hopkins Hospital (n=3116), Baylor College of Medicine (n=782), and the University of Michigan School of Medicine (n=235) were enrolled into this study. None of the patients had received preoperative hormonal or radiation therapy. <h3>Outcome Measures.</h3> —Simultaneous prediction of organ-confined disease, isolated capsular penetration, seminal vesicle involvement, or pelvic lymph node involvement using updated nomograms. <h3>Results.</h3> —Prostate-specific antigen level, TNM clinical stage, and Gleason score contributed significantly to the prediction of pathological stage (<i>P</i><.001). Bootstrap estimates of the median and 95% confidence interval of the predicted probabilities are presented in the nomograms. For most cells in the nomograms, there is a greater than 25% probability of qualifying for more than one of the pathological stages. In the validation analyses, 72.4% of the time the nomograms correctly predicted the probability of a pathological stage to within 10% (organ-confined disease, 67.3%; isolated capsular penetration, 59.6%; seminal vesicle involvement, 79.6%; pelvic lymph node involvement, 82.9%). <h3>Conclusions.</h3> —The data represent a multi-institutional modeling and validation of the clinical utility of combining PSA level measurement, clinical stage, and Gleason score to predict pathological stage for a group of men with localized prostate cancer. Clinicians can use these nomograms when counseling individual patients regarding the probability of their tumor being a specific pathological stage; this will enable patients and physicians to make more informed treatment decisions based on the probability of a pathological stage, as well as risk tolerance and the values they place on various potential outcomes.
ENZYMATIC DEBRIDEMENT OF THIRD-DEGREE BURNS ON GUINEA PIGS BY <i>CLOSTRIDIUM HISTOLYTICUM</i> PROTEINASES (1962)

Webster, Marion E. (Walter Reed Army Institute of Research, Washington, D. C.), Patricia L. Altieri, David A. Conklin, Sanford Berman, Joseph P. Lowenthal, and Raymond B. Gochenour. Enzymatic debridement of third-degree burns on guinea pigs by Clostridium histolyticum proteinases. J. Bacteriol. 83:602-608. 1962.-An attempt has been made to correlate in vitro activities of Clostridium histolyticum H-4 proteinases, as measured against azocasein, azocoll, gelatin, and collagen, with their ability to debride full-thickness third-degree burns (360 C, 15 sec) on guinea pigs. The major portion of the debriding activity is tentatively identified as due to the delta-proteinase, in the absence of cysteine, and to a new proteinase contained in the same fraction in the presence of cysteine. Other proteinases produced by this strain were also capable of debriding burns. However, collagenase and the gelatinase of the 0 to 22% fraction did not appear to be essential for the debridement of these burns.Studies of the proteinases produced by this organism have suggested that at least nine and probably more proteolytic enzymes are present. The need for more highly purified proteinases, in order to determine which enzyme(s) is responsible for debridement of guinea pig burns, is evident.
Occurrence of Steam Pops During Irrigated RF Ablation: Novel Insights from Microwave Radiometry (2013)

During irrigated RF ablation, steam pop occurrence can be predicted by both, the rate of rise and the maximum volumetric temperature measured by microwave radiometry.
Detailed analysis of the mean diameter and diameter distribution of single-wall carbon nanotubes from their optical response (2002)

We report a detailed analysis of the optical properties of single-wall carbon nanotubes (SWCNT's) with different mean diameters as produced by laser ablation. From a combined study of optical absorption, high-resolution electron energy-loss spectroscopy in transmission, and tight-binding calculations we were able to accurately determine the mean diameter and diameter distribution in bulk SWCNT samples. In general, the absorption response can be well described assuming a Gaussian distribution of nanotube diameters and the predicted inverse proportionality between the nanotube diameter and the energy of the absorption features. A detailed simulation enabled not only a determination of the mean diameter of the nanotubes, but also gives insight into the chirality distribution of the nanotubes. The best agreement between the simulation and experiment is observed when only nanotubes within $15\ifmmode^\circ\else\textdegree\fi{}$ of the armchair axis are considered. The mean diameters and diameter distributions from the optical simulations are in very good agreement with the values derived from other bulk sensitive methods such as electron diffraction, x-ray diffraction, and Raman scattering.
Panton-Valentine leukocidin positive community-acquired MRSA infection in Japan (2004)

In mid-June, Japanese media reported that a virulent strain of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA)
Developmental capability of denuded bovine oocyte in a Co‐culture system with intact cumulus‐oocyte complexes: Role of cumulus cells, cyclic adenosine 3′,5′‐monophosphate, and glutathione (2005)

Cumulus oophorus cells have been implicated in the regulation of female gamete development, meiotic maturation, and oocyte-sperm interaction. Nevertheless, the specific role of cumulus cells (CCs) during the final stages of oocyte maturation and fertilization processes still remains unclear. Several studies have been conducted in order to clarify the role of follicular cells using culture systems where denuded oocytes (DOs) were co-cultured with isolated CCs, or in the presence of conditioned medium. However, those attempts were ineffective and the initial oocyte competence to become a blastocyst after fertilization was only partially restored. Aim of the present study was to analyze the effect of the interactions between somatic cells and the female gamete on denuded oocyte developmental capability using a system of culture where CCs were present as dispersed CCs or as intact cumulus-oocyte complexes (COCs) in co-culture with oocytes freed of CC investment immediately after isolation from the ovary. Moreover, we analyzed the specific role of cyclic adenosine 3'-5' monophosphate (cAMP) and glutathione (GSH) during FSH-stimulated maturation of denuded oocyte co-cultured with intact COCs. Our data confirm that denuded oocyte has a scarce developmental capability, and the presence of dispersed CCs during in vitro maturation (IVM) does not improve their developmental competence. On the contrary, the co-presence of intact COCs during denuded oocyte IVM partially restores their developmental capability. The absence of CCs investment causes a drop of cAMP content in DOs at the beginning of IVM and the addition of a cAMP analog in the culture medium does not restore the initial oocyte developmental competence. The relative GSH content of denuded oocyte matured in presence of intact COCs is consistent with the partial recovery of their developmental capability. However, the complete restoration of a full embryonic developmental potential is achieved only when DOs are co-cultured with intact COCs during both IVM and in vitro fertilization (IVF). Our results suggest that the direct interaction between oocyte and CCs is not essential during IVM and IVF of denuded oocyte. We hypothesize that putative diffusible factor(s), produced by CCs and/or by the crosstalk between oocyte and CCs in the intact complex, could play a key role in the acquisition of developmental competence of the denuded female gamete.
The Clothoid Computation: A Simple and Efficient Numerical Algorithm (2016)

The clothoid (also known as Cornu spiral or Euler spiral) is a curve that is characterized by its curvature being proportional to its length. This property makes it very useful as a transition curve when designing the layout of roads and railway tracks. This paper presents an analysis of two methods for computing the clothoid: the classical method, which is based on the use of explicit formulas obtained from Taylor expansions of sine and cosine functions, and an alternative algorithm, which is based on the numerical solution of the initial value problems giving the clothoid parametrization. This alternative method is simple and efficient, and its effectiveness is shown through its application to three classical problems of horizontal road alignment.
Enhanced Viability of Corneal Epithelial Cells for Efficient Transport/Storage Using a Structurally Modified Calcium Alginate Hydrogel (2012)

Our novel methodology of controlling alginate gel shape and pore size together provides a more practical and economical alternative to established corneal tissue/cell storage methods.
Brain Plasticity Mechanisms and Memory: A Party of Four (2007)

A defining characteristic of the brain is its remarkable capacity to undergo activity-dependent functional and morphological remodeling via mechanisms of plasticity that form the basis of our capacity to encode and retain memories. Today, it is generally accepted that the neurobiological substrate of memories resides in activity-driven modifications of synaptic strength and structural remodeling of neural networks activated during learning. Since the discovery of long-term potentiation, the role of synaptic strengthening in learning and memory has been the subject of considerable investigation, and numerous studies have provided new insights into how this form of plasticity can subserve memory function. At the same time, other studies have explored the contribution of synaptic elimination or weakening; synaptogenesis, the growth of new synaptic connections and synapse remodeling; and more recently, neurogenesis, the birth and growth of new neurons in the adult brain. In this review, based on work in the hippocampus, the authors briefly outline recent advances in their understanding of the mechanisms and functional role of these four types of brain plasticity in the context of learning and memory. While they have long been considered as alternative mechanisms of plasticity underlying the storage of long-term memories, recent evidence suggests that they are functionally linked, suggesting the mechanisms underlying plasticity in the brain required for the formation and retention of memories are multifaceted.
Opioid requirement, opioid receptor expression, and clinical outcomes in patients with advanced prostate cancer (2013)

BACKGROUND Preclinical studies show that opioids stimulate angiogenesis and tumor progression through the mu opioid receptor (MOR). Although MOR is overexpressed in several human malignancies, the effect of chronic opioid requirement on cancer progression or survival has not been examined in humans. METHODS We performed a retrospective analysis on 113 patients identified in the Minneapolis VA Tumor Registry (test cohort) and 480 patients from the national VA Central Cancer Registry (validation cohort) who had been diagnosed with stage IV prostate cancer between 1995 and 2010 to examine whether MOR expression or opioid requirement is associated with disease progression and survival. All opioids were converted to oral morphine equivalents for comparison. Laser scanning confocal microscopy was used to analyze MOR immunoreactivity in prostate cancer biopsies. The effects of variables on outcomes were analyzed in univariable and multivariable models. RESULTS In patients with metastatic prostate cancer, MOR expression and opioid requirement were independently associated with inferior progression‐free survival (hazard ratio [HR] 1.65, 95% confidence interval [CI] 1.33‐2.07, P <.001 and HR 1.08, 95% CI 1.03‐1.13, P <.001, respectively) and overall survival (HR 1.55, 95% CI 1.20‐1.99, P <.001 and HR 1.05, 95% CI 1.00‐1.10, P = .031, respectively). The validation cohort confirmed that increasing opioid requirement was associated with worse overall survival (HR 1.005, 95% CI 1.002‐1.008, P = .001). CONCLUSION Higher MOR expression and greater opioid requirement are associated with shorter progression‐free survival and overall survival in patients with metastatic prostate cancer. Nevertheless, clinical practice should not be changed until prospective randomized trials show that opioid use is associated with inferior clinical outcomes, and that abrogation of the peripheral activities of opioids ameliorates this effect. Cancer 2013 ;119:4103–4110. © 2013 American Cancer Society .
Freedom and Comedy (1965)

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Limits on Replenishment of the Resting CD4+ T Cell Reservoir for HIV in Patients on HAART (2007)

Whereas cells productively infected with human immunodeficiency virus type 1 (HIV-1) decay rapidly in the setting of highly active antiretroviral therapy (HAART), latently infected resting CD4 T cells decay very slowly, persisting for the lifetime of the patient and thus forming a stable reservoir for HIV-1. It has been suggested that the stability of the latent reservoir is due to low-level viral replication that continuously replenishes the reservoir despite HAART. Here, we offer the first quantitative study to our knowledge of inflow of newly infected cells into the latent reservoir due to viral replication in the setting of HAART. We make use of a previous observation that in some patients on HAART, the residual viremia is dominated by a predominant plasma clone (PPC) of HIV-1 not found in the latent reservoir. The unique sequence of the PPC serves as a functional label for new entries into the reservoir. We employ a simple mathematical model for the dynamics of the latent reservoir to constrain the inflow rate to between 0 and as few as 70 cells per day. The magnitude of the maximum daily inflow rate is small compared to the size of the latent reservoir, and therefore any inflow that occurs in patients on HAART is unlikely to significantly influence the decay rate of the reservoir. These results suggest that the stability of the latent reservoir is unlikely to arise from ongoing replication during HAART. Thus, intensification of standard HAART regimens should have minimal effects on the decay of the latent reservoir.
Research on network security of defense based on Honeypot (2010)

With the development of the network attack technique, the increase of the security risk on the internet, each host in the network may be the target of the attack. Honeypot technology can proactively detect and respond to the intrusion and the attack of the network. Compared with other security mechanisms, it has the feature of using simply, configurations flexibly, occupying less resource, and working effectively in a complex environment, furthermore, all the collected data and information has a good relevant and study value, so that it can capture and analyze the characteristic, which can effectively limit the spread of the aggressive behavior on the network.
Neonatal pneumococcal conjugate vaccine immunization primes T cells for preferential Th2 cytokine expression: A randomized controlled trial in Papua New Guinea (2009)

The effects of neonatal immunization with 7-valent pneumococcal conjugate vaccine (7vPCV) on development of T-cell memory and general immune maturation were studied in a cohort of Papua New Guinean newborns. Neonatal 7vPCV priming (followed by a dose at 1 and 2 months of age) was associated with enhanced Th2, but not Th1, cytokine responses to CRM(197) compared to 7vPCV at 1 and 2 months of age only. T cell responses to non-7vPCV vaccine antigens were similar in all groups, but TLR-mediated IL-6 and IL-10 responses were enhanced in 7vPCV vaccinated compared to controls. Neonatal 7vPCV vaccination primes T cell responses with a polarization towards Th2 with no bystander effects on other T cell responses.
Occupational skin diseases in dental laboratory technicians (1996)

In Germany, occupational skin disease (OSD) in dental technicians (DT) has been steadily rising in recent years and causing considerable costs for medical care and rehabilitation. Our objective in this study was to: (i) examine affected workers; (ii) perform patch tests to identify causative agents; (iii) develop strategies of prevention. 7 dental laboratories were inspected as to materials used, working habits, safety regulations, etc. A computer data base was developed for products (trade name, active ingredient, additives, etc.). A questionnaire regarding development of OSD was sent out to 1132 dental technicians (45 questions). 55 DT with suspected OSD were examined and patch tested with the standard series, an extensive series of methacrylates, and own materials. Working conditions, and knowledge of potential hazards, varied greatly in the laboratories visited. The safety data sheets of working materials were of little use and required supplementation by the computer data base, which provided rapid access to allergological information (e.g., type of acrylate, concentration). In the questionnaire (173 answers), 36% reported skin lesions attributed to work and 1/3 suspected plastic materials as their primary cause. Among the 55 DT examined, allergic contact dermatitis was diagnosed in 63.6% and irritant contact dermatitis in 23.6%. Most of the allergens identified (74%) were found in plastic materials (methyl methacrylate (MMA), 9 patients (16%); 2-hydroxyethyl methacrylate (2-HEMA), 18 patients (33%); ethyleneglycol dimethacrylate (EGDMA), 15 patients (27%)). In 16 patients, multiple sensitizations to various methacrylates were found. The fingertips were primarily involved in allergic contact dermatitis (93%), whereas in irritant contact dermatitis, the dorsa of the fingers (especially of the dominant hand) were affected (80%). 9 patients also showed lesions on the face, neck and forearms. The main irritant factors included wet work, contact with plaster, mechanical friction and thermal changes. Based on experience with DT, various preventive measures have been tried and found to be effective (reduction of skin contact, 4H Gloves, etc.). In conclusion, better knowledge of OSD in dental laboratories (in physicians, DT and their employers) would lead to a reduced rate of new cases.
Effects on Performance of an Internal Heat Exchanger According to Charge Amount and Operating Condition in $CO_2$ Cooling Mode (2012)

This is an experimental study on the performance characteristics of effective heat pump in the cooling mode using a single-stage compression cycle with an IHX(internal heat exchanger). The performance of a single-stage compression with IHX was investigated according to charge amount and operating condition. Moreover, the performance characteristic of cooling operating was analyzed with the length of IHX. As a result, the optimum refrigerant charge amount was 2.2 kg. The optimal system COP for compressor frequency of 30, 40, 50, and 60 Hz was 3.493, 3.228, 2.978, and 2.659, respectively. Since the system with IHX can maintain large cooling capacity regardless of operating condition, the system performance doesn't reduce considerably under unfavorable condition. When the compressor frequency was 40 Hz, the COP for a system with IHX length of 3 m and 5 m was 3.361 and 3.51, respectively. By using the IHX into a cooling system, the performance and reliability improves simultaneously.