gebhart/patrepeval huggingface dataset:
Advancing a Human Onchocerciasis Vaccine From Antigen Discovery to Efficacy Studies Against Natural Infection of Cattle With Onchocerca ochengi (2022)

Human onchocerciasis is a devastating neglected tropical disease caused by infection of the filarial nematode <i>Onchocerca volvulus</i>. The infection can cause irreversible visual impairment or blindness and stigmatizing dermatitis. More than 32 million people were estimated to be infected with <i>O. volvulus</i> in Africa, and 385,000 suffered from blindness. Even though the implementation of mass drug administration (MDA) with ivermectin has reduced the global prevalence of onchocerciasis, <i>O. volvulus</i> infection remains challenging to control because MDA with ivermectin cannot be implemented in endemic areas co-endemic with loiasis due to the risk of severe adverse events. There is also emerging drug resistance to ivermectin that further complicates the elimination of onchocerciasis. Thus, the development of a vaccine that would induce protective immunity and reduce infection burden is essential. Efforts to develop prophylactic and/or therapeutic vaccines for onchocerciasis have been explored since the late 1980s by many researchers and entities, and here we summarize the recent advances made in the development of vaccines against the infection of <i>O. volvulus</i> and onchocerciasis.
Self-assembly of a π-electronic amphiphile consisting of a zinc porphyrin–fullerene dyad: formation of micro-vesicles with a high stability (2004)

An amphiphilic zinc porphyrin-fullerene dyad appended with triethyleneglycol chains in aqueous media forms uniformly-sized multilamellar vesicles with a mean diameter of 100 nm that are thermally stable and robust against membrane lysis with surfactants.
Effect of free and vesicle-bound cysteine proteinases of Porphyromonas gingivalis on plasma clot formation: implications for bleeding tendency at periodontitis sites (1995)

Infection by Porphyromonas gingivalis is strongly associated with adult periodontitis, with proteinases from this bacterium now considered to be important virulence factors. In order to investigate possible pathological functions of these enzymes, we examined the effect of both free and vesicle-bound forms of the two major cysteine proteinases (gingipains) of P. gingivalis on plasma clot formation by using thrombin time (TT) measurements. Both Lys-gingipain (gingipain-K) and Arg-gingipain (gingipain-R) prolonged plasma TT in a dose- and time-dependent manner, and this was also found with vesicles which are the biological carriers of P. gingivalis proteinases. The increase in plasma TT by vesicles could be completely reversed by treatment with nonspecific cysteine proteinase inhibitors but only partially by compounds selective for either gingipain-K or gingipain-R. Preincubation of vesicles with a gingipain-K-specific inhibitor (z-FK-ck) reduced plasma TT more than a gingipain-R-specific inhibitor (leupeptin), suggesting that under physiological conditions gingipain-K was more effective in fibrinogen destruction. Each purified enzyme also markedly increased fibrinogen TT, gingipain-R being fourfold more potent than gingipain-K. However, in plasma, gingipain-R was ineffective because of the inhibitory effect of albumin. These results imply that cysteine proteinases, especially gingipain-K, abrogate the clotting potential of fibrinogen and, therefore, may contribute to the bleeding tendency and to persistent inflammation in periodontitis sites infected with P. gingivalis.
Polarisation optics for biomedical and clinical applications: a review (2021)

Many polarisation techniques have been harnessed for decades in biological and clinical research, each based upon measurement of the vectorial properties of light or the vectorial transformations imposed on light by objects. Various advanced vector measurement/sensing techniques, physical interpretation methods, and approaches to analyse biomedically relevant information have been developed and harnessed. In this review, we focus mainly on summarising methodologies and applications related to tissue polarimetry, with an emphasis on the adoption of the Stokes-Mueller formalism. Several recent breakthroughs, development trends, and potential multimodal uses in conjunction with other techniques are also presented. The primary goal of the review is to give the reader a general overview in the use of vectorial information that can be obtained by polarisation optics for applications in biomedical and clinical research.
Lateral Patellofemoral Impingement: A Cause of Treatable Pain after TKA (2011)

Multiple etiologies may cause anterior knee pain after total knee arthroplasty. While prior studies have addressed component positioning and surgical technique, no series in the literature describes lateral patellofemoral impingement as a source of the pain. Over a 2-year period at our institution, 18 patients with 19 painful total knee arthroplasties were diagnosed with lateral patellofemoral impingement. All underwent revision surgery with either lateral facetectomy or revision of the patellar dome. These patients were followed with Knee Society scores for 1 year. Knee Society scores were significantly improved at 8 weeks, 16 weeks, and 1 year. Lateral patellofemoral impingement should always be considered in the differential diagnosis of the painful total knee arthroplasty. This should be evaluated clinically through direct palpation of the lateral facet, and radiographically with the sunrise view. Lateral facetectomy or patellar revision can be performed with predictably good clinical results.
Thermal Reversion Mechanism of N-Functionalized Merocyanines to Spiropyrans:  A Solvatochromic, Solvatokinetic, and Semiempirical Study (2000)

In continuing studies of the effect of solvent and molecular structure on the behavior of photochromic and thermochromic dye molecules, especially spiropyran (SP)−merocyanine (MC) interconversions, we have examined a series of 6‘-nitrobenzoindolinospiropyrans (6-nitro-BIPS) with varying N-functionalities (R = CH3, CH2CH2COOH, CH2CH2CH2SO3-, CH2CH2COO-Cholesteryl). The solvent effect was assessed by following the thermal decay of the photochemically ring-opened merocyanine to the spiropyran (MC ⇋ SP) via UV/vis spectroscopy at the λmax of the MC form. It was found that while modification of the N-moiety produced no perturbations in the solvatochromic behavior of these dyes, there was a marked effect on the solvatokinetic behavior. In nonpolar solvents, where the MCs possess predominantly quinoid character (unit central bond order), a constant thermal reversion rate was observed for the MCs with electron-rich N-ligands. This was attributed to electronic and steric interactions between the ligands and the phenoxide moiety. However, in polar solvents the increased zwitterionic character of the MCs (central bond order ∼2) leads to inhibition of the thermal reversion rate for the MCs in this study, independent of N-functionality. The MC ⇋ SP interconversion has also been examined by means of semiempirical calculations. These reveal the lowest energy pathway for conversion of the trans-MC to a cis-MC form via sequential bond rotation of the three central dihedral angles (α, β, and γ). The calculations support the observed solvatokinetic behavior, leading to the assignment of the trans/cis thermal isomerization as the rate-determining step in the overall process.
ChemInform Abstract: DIHYDROTHIOPHENES. 9. 2‐MERCAPTOALDEHYDE DIMERS AND 2,5‐DIHYDROTHIOPHENES FROM 1,3‐OXATHIOLAN‐5‐ONES (1983)

Abstract Die Umsetzung der Mercaptosäuren (I) mit dem Enolether (II) bzw. mit Aceton (III) führt zu den Thialactonen (IV), deren Reduktion Gemische mit den Komponenten (VI) und (VII) ergibt.
The Utility of Pitch Elevation in the Evaluation of Oropharyngeal Dysphagia: Preliminary Findings (2011)

Findings indicate that reduced pitch elevation can be indicative of reduced airway protection and swallowing impairment in some dysphagia patients and may be a useful supplement to dysphagia screening and diagnosis. Further investigation is warranted to determine the optimal utility of this procedure for different diagnostic categories of patients.
X‐ray crystal structure of a CRISPR‐associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8 (2009)

Page 528, lines 24–29: Furthermore, a complex of Ecoli subtype Cas proteins comprising Cse1, Cse2, Cse3, Cse4, and Cas5e,8 cleaves a ---------. Page 528, lines 38–42: This strain has another operon, TTHB160-161-162-163-164-165, encoding the RAMP (repeat-associated mysterious protein) module Cmr1–6 proteins8 on pTT27, which -------. Page 529, lines 1–4: In the present study, we determined the crystal structure of one of the functionally unknown RAMP module proteins, T. thermophilus Cmr5 (TTHB164), comprising a novel homotrimer. Page 531, lines 1–7 from the bottom of “Results and discussion” section: Furthermore, this structural feature is conserved in AF1862, although its basic patches are smaller than those of T. thermophilus Cmr5. It might be that Cmr5 interacts with DNA/RNA through its basic patches.
Hazardous Traffic Event Detection Using Markov Blanket and Sequential Minimal Optimization (MB-SMO) (2016)

The ability to identify hazardous traffic events is already considered as one of the most effective solutions for reducing the occurrence of crashes. Only certain particular hazardous traffic events have been studied in previous studies, which were mainly based on dedicated video stream data and GPS data. The objective of this study is twofold: (1) the Markov blanket (MB) algorithm is employed to extract the main factors associated with hazardous traffic events; (2) a model is developed to identify hazardous traffic event using driving characteristics, vehicle trajectory, and vehicle position data. Twenty-two licensed drivers were recruited to carry out a natural driving experiment in Wuhan, China, and multi-sensor information data were collected for different types of traffic events. The results indicated that a vehicle's speed, the standard deviation of speed, the standard deviation of skin conductance, the standard deviation of brake pressure, turn signal, the acceleration of steering, the standard deviation of acceleration, and the acceleration in Z (G) have significant influences on hazardous traffic events. The sequential minimal optimization (SMO) algorithm was adopted to build the identification model, and the accuracy of prediction was higher than 86%. Moreover, compared with other detection algorithms, the MB-SMO algorithm was ranked best in terms of the prediction accuracy. The conclusions can provide reference evidence for the development of dangerous situation warning products and the design of intelligent vehicles.
Vivid structural colors from long-range ordered and carbon-integrated colloidal photonic crystals (2018)

A facile strategy to prepare high-quality colloidal photonic crystals (PCs) with good visibility is proposed. Based on a high refractive-index material (zinc sulfide), highly monodispersed colloidal particles are successfully produced and assembled into long-range ordered crystalline colloidal arrays. The carbon-based materials are in situ incorporated with the long-range ordered colloidal PCs, which endows PCs with the combined characteristics to simultaneously achieve an intense photonic stop band and excellent control of incoherent light scattering. Owing to these merits, the obtained ZnS colloidal PCs have demonstrated strong brightness with the maximum reflectivity of 98%. Moreover, the coloration, saturation, and viewing angle are all improved. This study provides a straightforward and cost-effective strategy to create structural colors with high-quality visibility, which is expected to facilitate future applications of colloidal PCs.
Position measurement method for alignment in UV imprint using a high index mold and “electronic” moiré technique (2007)

In UV imprint, positioning errors can occur between a mold and a wafer due to pressure when there is a contact with the UV resin. The moiré technique, which is produced by superimposition of two gratings, is a well-known and simple method for high-resolution position measurement. However, the authors believe that a direct observation of two separate gratings is more appropriate for higher positioning accuracy. Here they propose a new method for the position measurement, which obtains “electronic” moiré fringes by combining the images of two separate gratings from different areas of the mold and the wafer. The fundamental detection error was σ=0.15nm. The repeatabilities of the total system was σ=0.68nm in air and σ=0.73nm in resin. The linearity of the measurement value to control signal was R2=0.97.
ChemInform Abstract: Total Synthesis of Furanocembranolides. Part 2. Macrocyclization Studies Culminating in the Synthesis of a Dihydropseudopterolide and Gorgiacerone. Related Furanocembranolide Interconversions. (1992)

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.
Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping (2010)

The model plant Arabidopsis thaliana exhibits extensive natural variation in resistance to parasites. Immunity is often conferred by resistance (R) genes that permit recognition of specific races of a disease. The number of such R genes and their distribution are poorly understood. In this study, we investigated the basis for resistance to the downy mildew agent Hyaloperonospora arabidopsidis ex parasitica (Hpa) in a global sample of A. thaliana. We implemented a combined genome-wide mapping of resistance using populations of recombinant inbred lines and a collection of wild A. thaliana accessions. We tested the interaction between 96 host genotypes collected worldwide and five strains of Hpa. Then, a fraction of the species-wide resistance was genetically dissected using six recently constructed populations of recombinant inbred lines. We found that resistance is usually governed by single dominant R genes that are concentrated in four genomic regions only. We show that association genetics of resistance to diseases such as downy mildew enables increased mapping resolution from quantitative trait loci interval to candidate gene level. Association patterns in quantitative trait loci intervals indicate that the pool of A. thaliana resistance sources against the tested Hpa isolates may be predominantly confined to six RPP (Resistance to Hpa) loci isolated in previous studies. Our results suggest that combining association and linkage mapping could accelerate resistance gene discovery in plants.
Entorhinal tau is associated with increased hippocampal activation and memory deficits in Alzheimer’s disease (2020)

Abstract Background To date, it remains unclear how the hallmark pathological changes of Alzheimer’s disease (AD), amyloid plaques, and neurofibrillary tangles, affect neuronal activity and, consequently, cognition. In cognitively normal aging, it appears that tau accumulation may drive hippocampal hyperactivity, however, studies investigating this association in AD are sparse. Method Patients with mild cognitive impairment (MCI) or mild dementia due to AD (n = 15) underwent positron emission tomography with the tracer [ 18 F]‐AV‐1451, which binds to tau accumulation, and performed a visual item memory task during functional magnetic resonance imaging. Result Entorhinal tau accumulation was highly correlated with memory‐related hippocampal activation. Greater tau accumulation and hippocampal activation were negatively correlated with memory performance. Neural activation in other task‐related structures was not correlated with local or global tau accumulation. Conclusion Similar to observations in cognitively healthy aging, entorhinal tau accumulation is closely associated with hippocampal hyperactivity and impaired memory performance in MCI and mild dementia. Interestingly, this association is specific for medial temporal lobe structures.
Notch filtering and multirate control for radial tracking in high-speed DVD-players (2002)

The problem considered in this paper is the radial tracking of the optical pick-up in a DVD-ROM player. For low-speed players, it is known that this problem can be solved by means of simple lead-lag regulators. For high-speed players, the servo design problem is more tricky, and a more sophisticated control architecture is required. The control scheme here proposed is constituted by a lead-lag filter and by two adapted notch filters. This set of filters is implemented in a parallel multirate structure. The resulting controller is simple, low-cost, and adequate to meet the required tracking-error specifications. The performance of the controller is tested on a real plant; experimental results are extensively reported.
Substrate Controlled Divergence in Polyketide Synthase Catalysis (2015)

Biochemical characterization of polyketide synthases (PKSs) has relied on synthetic substrates functionalized as electrophilic esters to acylate the enzyme and initiate the catalytic cycle. In these efforts, N-acetylcysteamine thioesters have typically been employed for in vitro studies of full PKS modules as well as excised domains. However, substrate engineering approaches to control the catalytic cycle of a full PKS module harboring multiple domains remain underexplored. This study examines a series of alternatively activated native hexaketide substrates on the catalytic outcome of PikAIV, the sixth and final module of the pikromycin (Pik) pathway. We demonstrate the ability to control product formation with greater than 10:1 selectivity for either full module catalysis, leading to a 14-membered macrolactone, or direct cyclization to a 12-membered ring. This outcome was achieved through modifying the type of hexaketide ester employed, demonstrating the utility of substrate engineering in PKS functional studies and biocatalysis.
Pseudomonas aeruginosa strain RW41 mineralizes 4‐chlorobenzenesulfonate, the major polar by‐product from DDT manufacturing (2008)

Pseudomonas aeruginosa RW41 is the first bacterial strain, which could be isolated by virtue of its capability to mineralize 4-chlorobenzenesulfonic acid (4CBSA), the major polar by-product of the chemical synthesis of 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane (DDT). This capability makes the isolate a promising candidate for the development of bioremediation technologies. The bacterial mineralization of 4CBSA proceeds under oxygenolytic desulfonation and transient accumulation of sulfite which then is oxidized to sulfate. High enzyme activities for the turnover of 4-chlorocatechol were measured. The further catabolism proceeded through 3-chloromuconate and, probably, the instable 4-chloromuconolactone, which is directly hydrolyzed to maleylacetate. Detectable levels of maleylacetate reductase were only present when cells were grown with 4CBSA. When the ordinary catechol pathway was induced during growth on benzenesulfonate, catechol was ortho-cleaved to cis,cis-muconate and a partially purified muconate cycloisomerase transformed it to muconolactone in vitro. The same enzyme transformed 3-chloro-cis,cis-muconate into cis-dienelactone (76%) and the antibiotically active protoanemonin (24%). These observations are indicative for a not yet highly evolved catabolism for halogenated substrates by bacterial isolates from environmental samples which, on the other hand, are able to productively recycle sulfur and chloride ions from synthetic haloorganosulfonates.
AXL targeting restores PD-1 blockade sensitivity of STK11/LKB1 mutant NSCLC through expansion of TCF1+ CD8 T cells (2022)

Mutations in <i>STK11/LKB1</i> in non-small cell lung cancer (NSCLC) are associated with poor patient responses to immune checkpoint blockade (ICB), and introduction of a <i>Stk11/Lkb1</i> (<i>L</i>) mutation into murine lung adenocarcinomas driven by mutant <i>Kras</i> and <i>Trp53</i> loss (<i>KP</i>) resulted in an ICB refractory syngeneic <i>KPL</i> tumor. Mechanistically this occurred because <i>KPL</i> mutant NSCLCs lacked TCF1-expressing CD8 T cells, a phenotype recapitulated in human <i>STK11/LKB1</i> mutant NSCLCs. Systemic inhibition of Axl results in increased type I interferon secretion from dendritic cells that expanded tumor-associated TCF1<sup>+</sup>PD-1<sup>+</sup>CD8 T cells, restoring therapeutic response to PD-1 ICB in <i>KPL</i> tumors. This was observed in syngeneic immunocompetent mouse models and in humanized mice bearing <i>STK11/LKB1</i> mutant NSCLC human tumor xenografts. NSCLC-affected individuals with identified <i>STK11/LKB1</i> mutations receiving bemcentinib and pembrolizumab demonstrated objective clinical response to combination therapy. We conclude that AXL is a critical targetable driver of immune suppression in <i>STK11/LKB1</i> mutant NSCLC.
A 16Gb 3b/ Cell NAND Flash Memory in 56nm with 8MB/s Write Rate (2008)

We present an 8 MB/s 3-bit per cell (D3) NAND flash memory that uses the same number of ECC bytes as 2-bit per cell (D2) NAND. Since no extra columns are added in D3 devices, the 16 Gb D3 chip in this paper achieves 0.112 Gb/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> compared to 0.079 Gb/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> on D2 chips, as previously reported (K. Takeuchi et al.,2006). This is a 41% improvement in Gb/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a 20% gain in overall die-size.
Automatic definition of surgical trajectories and acceptance window in pelvic trauma surgery using deformable registration (2018)

Purpose: Pelvic screw insertion for percutaneous fixation is a challenging surgical procedure that requires interpretation of complex 3D anatomy from 2D fluoroscopic images. Extensive surgical training is needed and trial and error often occurs in device placement, causing extended fluoroscopy time and increased radiation dose. A system is reported for automatic definition of acceptable surgical trajectories to facilitate guidance and quality assurance in a manner consistent with surgical workflow. Methods: An atlas was constructed with segmented pelvis shapes containing standard reference trajectories for screw placement. A statistical shape model computed from the atlas is used for deformable registration to the patient’s preoperative CT (without segmentation). By transferring the reference trajectories and surrounding acceptance windows (i.e., volumetric corridors of acceptable device placement) from the atlas, the system automatically computes reliable Kwire and screw trajectories for guidance (overlay in fluoroscopy) and QA. Results: A leave-one-out analysis was performed to evaluate the accuracy or registration and overlay. The registration achieved average surface registration accuracy of 1.82 &plusmn; 0.39 mm. Automatically determined trajectories conformed within acceptable cortical bone margins, maintaining 3.75 &plusmn; 0.68 mm distance from cortex in narrow bone corridors and demonstrating accurate registration and surgical trajectory definition without breaching cortex. Conclusions: The framework proposed in this work allows for multi-atlas based automatic planning of surgical trajectory without tracker or manual segmentation. The planning information can be further used to facilitate intraoperative guidance and post-operatively quality assurance in a manner consistent with surgical workflow.