gebhart/patrepeval huggingface dataset:
Figure S1 from Pharmacological TLR4 Antagonism Using Topical Resatorvid Blocks Solar UV-Induced Skin Tumorigenesis in SKH-1 Mice (2023)

&lt;p&gt;Staining for Ki67 in mouse tumors.&lt;/p&gt;
Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei (2015)

The filamentous fungus Trichoderma reesei has tremendous capability to secrete proteins. Therefore, it would be an excellent host for producing high levels of therapeutic proteins at low cost. Developing a filamentous fungus to produce sensitive therapeutic proteins requires that protease secretion is drastically reduced. We have identified 13 major secreted proteases that are related to degradation of therapeutic antibodies, interferon alpha 2b, and insulin like growth factor. The major proteases observed were aspartic, glutamic, subtilisin-like, and trypsin-like proteases. The seven most problematic proteases were sequentially removed from a strain to develop it for producing therapeutic proteins. After this the protease activity in the supernatant was dramatically reduced down to 4% of the original level based upon a casein substrate. When antibody was incubated in the six protease deletion strain supernatant, the heavy chain remained fully intact and no degradation products were observed. Interferon alpha 2b and insulin like growth factor were less stable in the same supernatant, but full length proteins remained when incubated overnight, in contrast to the original strain. As additional benefits, the multiple protease deletions have led to faster strain growth and higher levels of total protein in the culture supernatant.
Health economics in the field of osteoarthritis: An Expert's consensus paper from the European Society for Clinical and Economic Aspects of Osteoporosis and Osteoarthritis (ESCEO) (2013)

Better adherence to guidelines for economic evaluations is needed. There was strong support for the definition of a reference case and for what might constitute "standard optimal care" in terms of best clinical practice, for the control arms of interventional studies.
A Combination of Recombinant Mycobacterium bovis BCG Strains Expressing Pneumococcal Proteins Induces Cellular and Humoral Immune Responses and Protects against Pneumococcal Colonization and Sepsis (2017)

Pneumococcal diseases remain a substantial cause of mortality in young children in developing countries. The development of potentially serotype-transcending vaccines has been extensively studied; ideally, such a vaccine should include antigens that are able to induce protection against colonization (likely mediated by interleukin-17A [IL-17A]) and invasive disease (likely mediated by antibody). The use of strong adjuvants or alternative delivery systems that are able to improve the immunological response of recombinant proteins has been proposed but poses potential safety and practical concerns in children. We have previously constructed a recombinant <i>Mycobacterium bovis</i> BCG strain expressing a pneumococcal surface protein A (PspA)-PdT fusion protein (rBCG PspA-PdT) that was able to induce an effective immune response and protection against sepsis in a prime-boost strategy. Here, we constructed two new rBCG strains expressing the pneumococcal proteins SP 0148 and SP 2108, which confer IL-17A-dependent protection against pneumococcal colonization in mouse models. Immunization of mice with rBCG 0148 or rBCG 2108 in a prime-boost strategy induced IL-17A and gamma interferon (IFN-γ) production. The combination of these rBCG strains with rBCG PspA-PdT (rBCG Mix), followed by a booster dose of the combined recombinant proteins (rMix) induced an IL-17A response against SP 0148 and SP 2108 and a humoral response characterized by increased levels of IgG2c against PspA and functional antibodies against pneumolysin. Furthermore, immunization with the rBCG Mix prime/rMix booster (rBCG Mix/rMix) provides protection against pneumococcal colonization and sepsis. These results suggest the use of combined rBCG strains as a potentially serotype-transcending pneumococcal vaccine in a prime-boost strategy, which could provide protection against pneumococcal colonization and sepsis.
eNOS Gene Therapy Exacerbates Hepatic Ischemia-Reperfusion Injury in Diabetes (2006)

Previous studies indicate that endothelial nitric oxide synthase (eNOS) function is impaired in diabetes as a result of increased vascular generation of reactive oxygen species. We hypothesized that eNOS gene therapy would augment NO. bioavailability and protect against hepatic ischemia-reperfusion (I-R) injury in type 2 diabetes mellitus. We developed a transgenic (Tg) diabetic mouse in which eNOS is systemically overexpressed. We also examined the effects of hepatic eNOS adenovirus therapy in diabetic mice. Diabetic (db/db) and nondiabetic mice were subjected to hepatic I-R injury. In nondiabetic mice, genetic overexpression of eNOS (both eNOS-Tg and eNOS adenovirus) resulted in hepatoprotection. In contrast, hepatic I-R injury was significantly increased in the db/db eNOS-Tg mouse, as serum alanine aminotransaminase (ALT) levels were increased by 3.3-fold compared with diabetic controls. Similarly, eNOS adenovirus treatment resulted in a 3.2-fold increase in serum ALT levels as compared with diabetic controls. We determined that hepatic eNOS was dysfunctional in the db/db mouse and increased genetic expression of eNOS resulted in greater production of peroxynitrite. Treatment with the eNOS cofactor tetrahydrobiopterin (BH4) or the BH4 precursor sepiapterin resulted in a significant decrease in serum ALT levels following I-R injury. We present clear examples of the protective and injurious nature of NO. therapy in I-R. Our data indicate that eNOS exists in an "uncoupled" state in the setting of diabetes and that "recoupling" of the eNOS enzyme with cofactor therapy is beneficial.
Maze learning in aged rats is enhanced by phenserine, a novel anticholinesterase (1995)

A new generation of cholinesterase inhibitors is expected to overcome some limitations of the therapeutic use of anticholinesterases. Phenserine is a long-acting and selective inhibitor of acetylcholinesterase with a preferential brain uptake. We have assessed the effects of chronic phenserine tartrate treatment on performance of aged Fischer-344 rats in the 14-unit T-maze. Phenserine (1-3 mg kg-1, i.p.) treatment for 5 days significantly reduced the number of errors made in the Stone maze. Other performance variables were also improved. No side effects were noted across 5 days treatment at doses of 1-2 mg kg-1. Phenserine can therefore improve the performance of aged rats in this complex maze task without producing obvious side effects.
Mechanical Properties of Chest Protectors and the Likelihood of Ventricular Fibrillation Due to Commotio Cordis (2007)

Sudden death resulting from ventricular fibrillation (VF) caused by a nonpenetrating chest wall impact, known as commotio cordis (CC), is the second leading cause of death among young athletes. To date, seven young athletes wearing chest protectors have died from CC. The purpose of this study was to determine whether a relationship exists between mechanical properties of chest protectors and occurrence of VF, previously determined by Weinstock et al., using an established swine model. A servo-hydraulic material tester was used to determine properties of the chest protectors, including displacement, permanent deformation, stiffness, and area of pressure distribution. These properties were then compared with the occurrence of VF. We found that a decreased proportion of hits resulting in VF was significantly associated (R2 = 0.59, p = 0.001) with an increase in the area of pressure distribution. These findings are a limited, but crucial, first step in understanding the prevention of this complex and perplexing phenomenon.
JAAL-Net: a joint attention and adversarial learning network for skin lesion segmentation (2023)

<i>Objective.</i>Skin lesion segmentation plays an important role in the diagnosis and treatment of melanoma. Existing skin lesion segmentation methods have trouble distinguishing hairs, air bubbles, and blood vessels around lesions, which affects the segmentation performance.<i>Approach.</i>To clarify the lesion boundary and raise the accuracy of skin lesion segmentation, a joint attention and adversarial learning network (JAAL-Net) is proposed that consists of a generator and a discriminator. In the JAAL-Net, the generator is a local fusion network (LF-Net) utilizing the encoder-decoder structure. The encoder contains a convolutional block attention module to increase the weight of lesion information. The decoder involves a contour attention to obtain edge information and locate the lesion. To aid the LF-Net generate higher confidence predictions, a discriminant dual attention network is constructed with channel attention and position attention.<i>Main results.</i>The JAAL-Net is evaluated on three datasets ISBI2016, ISBI2017 and ISIC2018. The intersection over union of the JAAL-Net on the three datasets are 90.27%, 89.56% and 80.76%, respectively. Experimental results show that the JAAL-Net obtains rich lesion and boundary information, enhances the confidence of the predictions, and improves the accuracy of skin lesion segmentation.<i>Significance.</i>The proposed approach effectively improves the performance of the model for skin lesion segmentation, which can assist physicians in accurate diagnosis well.
Biomechanical evaluation of diabetic foot through hierarchical cluster analysis (2014)

Type 2 diabetes is predicted to become the 7th leading cause of death in the world by the year 2030 [1]. Diabetic foot is the most common long-term diabetic complication, and it is a major risk factor for plantar ulceration (PU), it is determined by peripheral neuropathy (PN), vascular disease, increased foot pressures, foot trauma, deformity and callus [1].

The aim of this study is to develop a methodology for automatic detection of patients at risk for PU based on 3 dimensional (3D) multisegment foot biomechanics through cluster analysis.
Thermal properties of a tough, new semicrystalline polyimide (1993)

Abstract Thermal properties of a new semicrystalline polyimide synthesized from 3,3′,4,4′‐benzophenonetetracarboxylic dianhydride ( BTDA ) and 2,2‐dimethyl‐1,3‐(4‐aminophenoxy)propane ( DMDA ) have been studied. Heat capacities in the solid and liquid states of BTDA ‐ DMDA have been measured. The heat capacity increase at the glass transition temperature ( T g = 230°C) is 145 J/°Cmol for amorphous BTDA ‐ DMDA . The equilibrium heat of fusion of the BTDA ‐ DMDA crystals has been obtained using wide‐angle X‐ray diffraction and differential scanning calorimetry measurements, and is 75.8 kj/mol. Based on the information on crystallinity and the heat capacity increase at T g , a rigid amorphous fraction is identified in semicrystalline BTDA ‐ DMDA samples, which represents an interfacial region between the crystalline and amorphous states. In particular, this fraction increases with the crystallinity of the sample, which should be associated with crystal sizes, and therefore with crystal morphology. It has also been found that this polymer has a high‐temperature crystal phase upon annealing above its original melting temperature. The thermal degradation activation energies of BTDA ‐ DMDA in nitrogen and air are determined to be 154 and 150kJ/mol, respectively.
Risk Factors for Prolonged Opioid Use and Effects of Opioid Tolerance on Clinical Outcomes After Anterior Cervical Discectomy and Fusion Surgery (2020)

4.
Carrier-induced optical bistability in silicon ring resonators (2006)

We demonstrate optical bistability in a micrometer-sized silicon ring resonator based on the free-carrier dispersion effect in silicon. We measure the transfer function of the resonator showing a hysteresis loop with an input optical power of less than 10 mW. The influence of the thermal optical effect, which is minimized in the experiment by use of nanosecond pulses, is evaluated theoretically. Applications include sequential logic operations for all-optical routing.
Multicycle Ozonation+Bioremediation for Soils Containing Residual Petroleum (2019)

We systematically assessed the removal of total petroleum hydrocarbons (TPHs) and other organic carbon using sequential biodegradation and ozonation in two soils (BM3 and BM4). We optimized the conditions for each step: 5% moisture content for ozonation and 10% moisture and circumneutral pH for biodegradation. For the relatively biodegradable TPH in BM3, preozonation and postozonation strategies were equally effective. In contrast, the more recalcitrant TPH in BM4 was better treated using postozonation. Carbon analyses along the treatment timeline revealed that dissolved organic carbon (DOC) was the dominant substrate for microbial consumption when readily biodegradable TPH was no longer available. The carbon in TPH was more reactive with O3 than was the rest of dichloromethane-extractable organic carbon (DeOC), and the fate of TPH dictated the changes of DeOC. However, the fate of total organic carbon was controlled mainly by the microbial mineralization of DOC. Ozonation did not directly enhance the biodegradation rate of the residual TPH after ozonation, but ozone converted TPH into DOC that was microbially mineralized. This is the first study that compares the efficiencies of pre- and postozonation of two distinctly different soils. This study provides insights regarding the fundamental mechanism through which biodegradation and ozonation integrate and reveals the dynamics between ozonation and biodegradation during treatment petroleum-contaminated soils. Multistage ozonation+biodegradation is a useful tool to achieve the regulatory TPH standard (10,000 mg/kg), and DOC should be measured alongside TPH to gauge the dynamics of the integrated process.
Surface‐Plasmon‐Enhanced Band Emission of ZnO Nanoflowers Decorated with Au Nanoparticles (2012)

A simple strategy was used to enhance band emission through the transfer of defect emission from ZnO to Au by using the energy match between the defect emission of ZnO and the surface plasmon absorbance of Au NPs through decorating the surface of ZnO nanoflowers with Au nanoparticles (Au NPs). The ZnO nanostructure, which was comprised of six nanorods that were attached on one side in a flower-like fashion, was synthesized by using a hydrothermal method. The temperature-dependent morphology and detailed growth mechanism were studied. The influence of the density of the Au NPs that were deposited onto the surface of ZnO on photoluminescence was investigated to optimize the configuration of the ZnO/Au system in terms of the maximum band emission. The sequential transfer of defect energy from ZnO to Au and electron transfer from excited Au to ZnO was proposed as a possible mechanism for the enhanced band emission.
Novel Techniques in Epilepsy Management: Venous Pacing and Capture of Electrical Activity in the Primate Cortex (2016)

New electrode design can be maneuvered safely in the venous system, provide adequate cortical tissue contact to record signals, detect these signals as normal or abnormal, successfully stimulate the cortex, and capture cortical tissue. These novel devices merit further study in chronic baboons to establish long-term efficacy of continuous seizure recording.
The design of a ferrofluid magnetic pipette (1997)

An electromagnetic pipette using a ferrofluid was designed to sample liquid volumes smaller than 0.2 microliter. Submicroliter sample sizes are desirable for reducing the amount of costly reagents and reducing sample requirement for large-scale analysis. The pipette consists of four electromagnets arranged such that air-gaps are aligned to accommodate a tube. A light-hydrocarbon-based ferrofluid is contained in the tube and acts as a plunger. The position of the ferrofluid in the tube was controlled to within 0.2 mm by combining adjacent air-gap magnetic fields. The position of the ferrofluid as a function of time and magnetic pressure as a function of position was measured in one electromagnet air-gap from the device. Maximum pressure measured was 770 Pa which corresponds to a maximum velocity of 0.9 cm/s. The assembled pipette weighs approximately 25 g, and it measures 4 cm long, 1 cm wide, and 3 cm high.
Life‐Cycle Costing Promotes Use of Corrosion‐Resistant Alloys (2016)

The use of “life-cycle costing” makes it more likely that durable and maintenance-free corrosion resistant alloys will be chosen. The cost of corrosion failure is examined and compared with raw material costs, and the excess cost of using lower initial cost, but inadequate material is explored. The desirability of using suitable corrosion-resistant alloys is highlighted. The use of life-cycle costing (LCC) to justify the use of materials with higher initial cost is illustrated.
RHYTHMS IN BLUE‐LIGHT‐INDUCED CONIDIATION OF WILD TYPE AND A MUTANT STRAIN OF Trichoderma harzianum (1988)

Abstract— Trichoderma harzianum normally requires light for conidiation. Conidiation of colonies grown in continuous light does not appear to be rhythmic, but sharp banding patterns are formed under light/dark cycles. A single pulse of blue light produces a sharp band of conidia that forms where the growing edge of the mycelia is located at the time when the light is given. A period of about 24 h is required following the light pulse to produce mature conidia. During this time colonies are insensitive to further induction by light. The fluence required to produce 50% saturation varies by a factor of about 3 depending on when the pulse is given. This change of sensitivity is rhythmic with a period length of approximately 27 h when grown on medium containing deoxycholate. The pattern of conidiation in a mutant strain (B119), which is able to form conidia in the dark, is rhythmic and the period length is dependent on the composition of the medium. Addition of deoxycholate to the medium increased the interval between dark bands from 12 to 24 h. The rhythmic banding is suppressed in constant light and a double banding pattern is produced in light/dark cycles. A pulse of blue light induces a band of conidia in this mutant, as in the wild type, but it also delays the reappearance of the dark banding pattern. The extent of this delay depends on when the pulse is given and, although the period length of the dark conidiation rhythm is affected by deoxycholate, the effect of blue light on its phase is not. Of the various rhythmic responses of Trichoderma studied here. the delay in reappearance of the dark banding pattern in B119 is the most promising for further detailed studies, for example of wavelength and temperature dependence.
Affinity-Guided Design of Caveolin-1 Ligands for Deoligomerization (2016)

Caveolin-1 is a target for academic and pharmaceutical research due to its many cellular roles and associated diseases. We report peptide WL47 (1), a small, high-affinity, selective disrupter of caveolin-1 oligomers. Developed and optimized through screening and analysis of synthetic peptide libraries, ligand 1 has 7500-fold improved affinity compared to its T20 parent ligand and an 80% decrease in sequence length. Ligand 1 will permit targeted study of caveolin-1 function.
Television advertising, not viewing, is associated with negative dietary patterns in children (2015)

The link between television viewing and poor diet was strongest for children who watched the most commercial television, and those who were actually exposed to advertisements embedded within programs. This association between advertisement exposure and poor diet emphasizes the need for public policy intervention to reduce children's food advertising exposures.
Leptin: Is It Important in Diabetes? (1996)

Obesity is a widespread and growing problem in developed nations such as Australia,' USA,Z France and the UK3 and is rapidly becoming an equal or greater problem in many developing populations and disadvantaged communities as a result of modernization or 'Cocacolonization'.',2The economic burden of obesity and associated disorders such as cardiovascular disease and non-insulin-dependent (Type 2) diabetes mellitus (NIDDM) was estimated to approach US$69 billion per annum in the USA in 1993 in health care costs, with a further US933 billion spent on fashionable diet programmes, books and 'instant cures '.4 Obesity confers a minimum three-to ten-fold risk of NIDDM and an increased risk of cardiovascular disease.It is associated with an array of other disorders including arthropathies, although these may be due to other risk
Development of dynamic multi-layered bioprocess models (2012)

Advances in experimental technologies in conjunction with the increasing number of sequenced genomes permitted uncovering new molecular interactions aiding in the characterization of individual cellular components. Until recently, in bioprocess engineering, cells were modeled as black box entities responsible for consuming substrates and producing certain compounds, ignoring the underlying biological mechanisms. Nonetheless, the development of cellular mechanistic dynamic models has been hampered by the lack of specific experimental data and imprecise knowledge of the mechanistic rate laws underlying several reactions. This fact hardens the applicability of engineering concepts to cellular systems. Even incomplete cellular models provide valuable insights to help consolidate ongoing efforts in Biotechnology, namely, the growing tendency in industry to replace chemical synthesis techniques by biotechnological ones. These tendencies are driven by sustainability and profitability concerns, regarding the production of certain chemical compounds like bulk chemicals and pharmaceuticals. It is important to bear in mind that the metabolism of wild-type microorganisms is geared to its survival and reproduction without engaging in the production of compounds outside this scope. Thus, the metabolism usually has to be modified in order to meet the desired industrial outcome, typically the overproduction of a target compound. In this work an optimization algorithm based on Evolutionary Computation approaches was previously developed in order to enhance the production of a target metabolite based on a dynamic metabolic model. An extension of mechanistic Escherichia coli model is currently being developed in order to study how to improve the production of industrial relevant compounds.
Optical Layer Failures in a Large Backbone (2016)

We analyze optical layer outages in a large backbone, using data for over a year from thousands of optical channels carrying live IP layer traffic. Our analysis uncovers several findings that can help improve network management and routing. For instance, we find that optical links have a wide range of availabilities, which questions the common assumption in fault-tolerant routing designs that all links have equal failure probabilities. We also find that by monitoring changes in optical signal quality (not visible at IP layer), we can better predict (probabilistically) future outages. Our results suggest that backbone traffic engineering strategies should consider current and past optical layer performance and route computation should be based on the outage-risk profile of the underlying optical links.
Synthetic Genomes (2020)

DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.