gebhart/patrepeval huggingface dataset:
The occurrence of human placental alkaline phosphatase (PLAP) in extracts of normal, benign and malignant tissues of the female genital tract. (1985)

In addition to its presence in extracts of carcinomatous tissues from the vulva, endometrium and ovary, PLAP can also be found in tissue extracts of benign conditions of the endometrium and myometrium. We detected slightly elevated levels of PLAP in patients with myoma, raised levels in 2/2 patients with endometrial polyps and high values in 2/2 patients with glandulocystic hyperplasia. Moreover, normal endometrium and fragments of normal Fallopian tube also contained fairly high amounts of endogenous PLAP. These results have important implications with regard to the possible use of PLAP as a tumour marker or of anti-PLAP monoclonal antibodies in radioimmunolocalization or radioimmunotherapy.
Human Multi-Compartment Airways-on-Chip Platform for Emulating Respiratory Airborne Transmission: From Nose to Pulmonary Acini (2022)

The past decade has witnessed tremendous endeavors to deliver novel preclinical <i>in vitro</i> lung models for pulmonary research endpoints, including foremost with the advent of <i>organ-</i> and <i>lung-on-chips</i>. With growing interest in aerosol transmission and infection of respiratory viruses within a host, most notably the SARS-CoV-2 virus amidst the global COVID-19 pandemic, the importance of crosstalk between the different lung regions (i.e., extra-thoracic, conductive and respiratory), with distinct cellular makeups and physiology, are acknowledged to play an important role in the progression of the disease from the initial onset of infection. In the present Methods article, we designed and fabricated to the best of our knowledge the first multi-compartment human <i>airway-on-chip</i> platform to serve as a preclinical <i>in vitro</i> benchmark underlining regional lung crosstalk for viral infection pathways. Combining microfabrication and 3D printing techniques, our platform mimics key elements of the respiratory system spanning (i) nasal passages that serve as the alleged origin of infections, (ii) the mid-bronchial airway region and (iii) the deep acinar region, distinct with alveolated airways. Crosstalk between the three components was exemplified in various assays. First, viral-load (including SARS-CoV-2) injected into the apical partition of the nasal compartment was detected in distal bronchial and acinar components upon applying physiological airflow across the connected compartment models. Secondly, nebulized viral-like dsRNA, poly I:C aerosols were administered to the nasal apical compartment, transmitted to downstream compartments via respiratory airflows and leading to an elevation in inflammatory cytokine levels secreted by distinct epithelial cells in each respective compartment. Overall, our assays establish an <i>in vitro</i> methodology that supports the hypothesis for viral-laden airflow mediated transmission through the respiratory system cellular landscape. With a keen eye for broader end user applications, we share detailed methodologies for fabricating, assembling, calibrating, and using our multi-compartment platform, including open-source fabrication files. Our platform serves as an early proof-of-concept that can be readily designed and adapted to specific preclinical pulmonary research endpoints.
Identification and functional characterization of polymorphisms in human cyclooxygenase-1 (PTGS1) (2020)

Cyclooxygenase-1 (COX-1, PTGS1) catalyzes the conversion of arachidonic acid to prostaglandin H2, which is subsequently metabolized to various biologically active prostaglandins. We sought to identify and characterize the functional relevance of genetic polymorphisms in PTGS1.
Recent advances in holmium doped fibers for high-energy lasers (Conference Presentation) (2018)

Holmium doped fiber lasers (HoDFL) are attractive candidates for high energy lasers used in directed energy applications because they operate at wavelengths that are safer to the eye. The common solution-doping technique for making HoDFs can result in the incorporation of hydroxyl (OH) impurity in the active fiber core. The HoDFL operational wavelength of ~2.0 µm is near the 2.2 µm combination absorption band of the OH fundamental mode and the SiO4 tetrahedron vibration, so the OH concentration must be <1 ppm to prevent degradation of the laser performance. We have routinely fabricated HoDF with [OH] < 0.5 ppm. We have developed an ultralow OH processing technique based on both atmospheric exclusion from the silica core soot preform and careful, extensive drying. We report a resonantly-pumped solution doped Ho3+ fiber laser with a slope efficiency of 74%, and an output power of 96W. We are also investigating nanoparticle (NP) doping, where the holmium ions are encaged in a nanoparticle host selected for properties such as low phonon energy, where they are shielded from the Silica lattice. By optimizing variables such as precursor concentrations, NP ripening times, and surfactant selection during synthesis we have been able to increase the Ho NP concentration levels in Silica fiber cores. This has also allowed us to increase concentrations of otherwise incompatible low phonon energy host materials into the cores of the fibers. Cores comprising Ho doped LaF3 and Lu2O3 nanoparticles exhibited slope efficiencies as high as 85% at 2.06 µm in a MOPA configuration.
Programmed death ligand 1 is over‐expressed by neutrophils in the blood of patients with active tuberculosis (2011)

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's largest infectious disease problems. Despite decades of intensive study, the immune response to Mtb is incompletely characterised, reflecting the extremely complex interaction between pathogen and host. Pathways that may alter the balance between host protection and pathogenesis are therefore of great interest. One pathway shown to play a role in the pathogenesis of chronic infections, including TB, is the programmed death-1 (PD-1) pathway. We show here that the expression of the programmed death ligand 1 (PD-L1), which interacts with PD-1, is increased in whole blood from active TB patients compared with whole blood from healthy controls or Mtb-exposed individuals, and that expression by neutrophils is largely responsible for this increase.
4‐(Dimethylamino)pyridine N‐oxide (DMAPO): An Effective Nucleophilic Catalyst in the Peptide Coupling Reaction with 2‐Methyl‐6‐nitrobenzoic Anhydride (2008)

Various carboxamides or peptides were synthesized from the corresponding carboxylic acids and amines or alpha-amino acids in high yields by the catalysis of 4-(dimethylamino)pyridine N-oxide (DMAPO) with 2-methyl-6-nitrobenzoic anhydride (MNBA). Because the segment-coupling reaction of alpha-amino acids proceeds through the effective activation of the carboxylic acid moieties with DMAPO in the presence of tertiary amines under mild conditions, undesired racemization was hardly observed in the synthesis of oligopeptides such as Z-Gly-Phe-Val-OMe, Z-Phe-Val-Ala-OMe, and Bz-Val-Val-OMe.
Parts-Per-Billion Carbon Monoxide Sensing in Silicon-on-Sapphire Mid-Infrared Photonic Crystal Waveguides (2018)

We experimentally detect 3 ppm carbon monoxide via optical absorbance in a 1mm long slotted photonic crystal waveguide in silicon-on-sapphire at wavelength λ= 4.55µm. Feasibility of low ppb sensing will be shown by design modifications.
Functional antenna integrated with relative humidity sensor using synthesised polyimide for passive RFID sensing (2007)

A new type of antenna with an RH (relative humidity) sensing function using a modified polyimide is proposed for passive RFID sensing. Designed to operate at a frequency that depends on the relative humidity level, the proposed antenna is a passive device that physically and functionally combines an antenna with an RH sensor. The compactness and cost-efficiency of the antenna enables it to realise a passive tag of the RFID sensing without an additional sensor component.
Cardiac remodelling – Part 2: Clinical, imaging and laboratory findings. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology (2022)

In patients with heart failure, the beneficial effects of drug and device therapies counteract to some extent ongoing cardiac damage. According to the net balance between these two factors, cardiac geometry and function may improve (reverse remodelling, RR) and even completely normalize (remission), or vice versa progressively deteriorate (adverse remodelling, AR). RR or remission predict a better prognosis, while AR has been associated with worsening clinical status and outcomes. The remodelling process ultimately involves all cardiac chambers, but has been traditionally evaluated in terms of left ventricular volumes and ejection fraction. This is the second part of a review paper by the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology dedicated to ventricular remodelling. This document examines the proposed criteria to diagnose RR and AR, their prevalence and prognostic value, and the variables predicting remodelling in patients managed according to current guidelines. Much attention will be devoted to RR in patients with heart failure with reduced ejection fraction because most studies on cardiac remodelling focused on this setting.
Characterization of skin lesion texture in diffuse reflectance spectroscopic images (2002)

This paper examines various texture features extracted from skin lesion images obtained by using diffuse reflectance spectroscopic imaging. Different image texture features have been applied to such images to separate precancerous from benign cases. These features are extracted based on the co-occurrence matrix, wavelet decomposition , fractal signature, and granulometric approaches. The results so far indicate that fractal and wavelet-based features are effective in distinguishing precancerous from benign cases.
Optical sensor for the detection of explosives: example of a fluorescent material (2009)

This paper deals with the detection of nitroaromatic explosives. A specific fluorescent material is devoted to the detection of ultra traces of explosives remaining on clothes. The sensor exhibits a large sensitivity for TNT or DNT vapors.
Functional Overlap of Microtubule Assembly Factors in Chromatin-Promoted Spindle Assembly (2009)

Distinct pathways from centrosomes and chromatin are thought to contribute in parallel to microtubule nucleation and stabilization during animal cell mitotic spindle assembly, but their full mechanisms are not known. We investigated the function of three proposed nucleation/stabilization factors, TPX2, gamma-tubulin and XMAP215, in chromatin-promoted assembly of anastral spindles in Xenopus laevis egg extract. In addition to conventional depletion-add back experiments, we tested whether factors could substitute for each other, indicative of functional redundancy. All three factors were required for microtubule polymerization and bipolar spindle assembly around chromatin beads. Depletion of TPX2 was partially rescued by the addition of excess XMAP215 or EB1, or inhibiting MCAK (a Kinesin-13). Depletion of either gamma-tubulin or XMAP215 was partially rescued by adding back XMAP215, but not by adding any of the other factors. These data reveal functional redundancy between specific assembly factors in the chromatin pathway, suggesting individual proteins or pathways commonly viewed to be essential may not have entirely unique functions.
Fluorinated Covalent Organic Polymers for High Performance Sulfur Cathodes in Lithium–Sulfur Batteries (2019)

Lithium–sulfur (Li–S) batteries by far offer higher theoretical energy density than that of the commercial lithium-ion battery counterparts, but suffer predominantly from an irreversible shuttling process involving lithium polysulfides. Here, we report a fluorinated covalent organic polymer (F-COP) as a template for high performance sulfur cathodes in Li–S batteries. The fluorination allowed facile covalent attachment of sulfur to a porous polymer framework via nucleophilic aromatic substitution reaction (SNAr), leading to high sulfur content, e.g., over 70 wt %. The F-COP framework was microporous with 72% of pores within three well-defined pore sizes, viz. 0.58, 1.19, and 1.68 nm, which effectively suppressed polysulfide dissolution via steric and electrostatic hindrance. As a result of the structural features of the F-COP, the resulting sulfur electrode exhibited high electrochemical performance of 1287.7 mAh g–1 at 0.05C, 96.4% initial Columbic efficiency, 70.3% capacity retention after 1000 cycles at 0.5C, and robust operation for a sulfur loading of up to 4.1 mgsulfur cm–2. Our findings suggest the F-COP family with the adaptability of SNAr chemistry and well-defined microporous structures as useful frameworks for highly sustainable sulfur electrodes in Li–S batteries.
Behavior of the N-Terminal Helices of the Diphtheria Toxin T Domain during the Successive Steps of Membrane Interaction (2007)

During intoxication of a cell, the translocation (T) domain of the diphtheria toxin helps the passage of the catalytic domain across the membrane of the endosome into the cytoplasm. We have investigated the behavior of the N-terminal region of the T domain during the successive steps of its interaction with membranes at acidic pH using tryptophan fluorescence, its quenching by brominated lipids, and trypsin digestion. The change in the environment of this region was monitored using mutant W281F carrying a single native tryptophan at position 206 at the tip of helix TH1. The intrinsic propensity to interact with the membrane of each helix of the N-terminus of the T domain, TH1, TH2, TH3, and TH4, was also studied using synthetic peptides. We showed the N-terminal region of the T domain was not involved in the binding of the domain to the membrane, which occurred at pH 6 mainly through hydrophobic effects. At that stage of the interaction, the N-terminal region remained strongly solvated. Further acidification eliminated repulsive electrostatic interactions between this region and the membrane, allowing its penetration into the membrane by attractive electrostatic interactions and hydrophobic effects. The peptide study indicated the nature of forces contributing to membrane penetration. Overall, the data suggested that the acidic pH found in the endosome not only triggers the formation of the molten globule state of the T domain required for membrane interaction but also governs a progressive penetration of the N-terminal part of the T domain in the membrane. We propose that these physicochemical properties are necessary for the translocation of the catalytic domain.
A Novel Approach to Quantum Heuristics for Structured Database Search (2001)

An algorithm for structured database searching is presented and used to solve the set partition problem. O(n) oracle calls are required in order to obtain a solution, but the probability that this solution is optimal decreases exponentially with problem size. Each oracle call is followed by a measurement, implying that it is necessary to maintain quantum coherence for only one oracle call at a time.
CX3CL1-Fc treatment prevents atherosclerosis in Ldlr KO mice (2018)

These results indicate that CX3CL1-Fc can inhibit monocyte/endothelial cell adhesion as well as reduce atherosclerosis.
Use of clustering with partial least squares regression for predictions based on hyperspectral data (2014)

Visible and near-infrared (VNIR) diffuse reflectance spectroscopy (DRS) has proven to be effective tools of estimation of soil properties. Regression models are usually calibrated on the entire datasets without its stratification. This paper discusses how clustering of the soil spectra improves prediction of basic soil properties: contents of sand, clay, soil organic carbon (SOC) and total nitrogen, as well as the cation exchange capacity (CEC) and total exchangeable bases (TEB). The analysis was performed on a set of 212 soil samples collected from surface horizons throughout the area of arable lands in Poland. Spectral measurements were done using ASD Fildspec PRO with attached Source Probe Mug-Lite in the wavelength range of 350-2500 nm. First, partial least squares (PLS) regression models using the raw spectra and their first derivatives were calibrated on the entire dataset. Then, the observations (soil samples) were clustered using the Ward and K-mean methods based both on the raw and the transformed spectral data. The PLS regression modeling fitted separately within each cluster was performed. Our findings indicate that clustering is potentially useful to enhance the prediction of soil properties based on the DSR data when using the PLS regression modeling. In a practical application to a given set of soil samples, one needs to implement a two-step procedure recommended in this paper. In the first step, one runs a cross-validation analysis in order to identify the best combination of the spectra transformation, the type of the clustering method, and the number of clusters. In the second step, the best combination is applied to the whole dataset for prediction purposes. The improvement achieved by the described procedure ranges from 24 to 49 % reduction in the cross validation root mean squared error.
Design, immunogenicity, and efficacy of a pan-sarbecovirus dendritic-cell targeting vaccine (2021)

Abstract The emergence of SARS-CoV-2 variants of concern (VOCs) that escape pre-existing antibody neutralizing responses increases the need for vaccines that target conserved epitopes and induce cross-reactive B- and T-cell responses. We used a computational approach and sequence alignment analysis to design a new-generation subunit vaccine targeting conserved sarbecovirus B- and T-cell epitopes from Spike (S) and Nucleocapsid (N) to antigen-presenting cells expressing CD40 (CD40.CoV2). We demonstrate the potency of CD40.CoV2 to elicit high levels of cross-neutralizing antibodies against SARS-CoV-2, VOCs, and SARS-CoV-1 in K18-hACE2 transgenic mice, associated with improved viral control and survival after challenge. In addition, we demonstrate the potency of CD40.CoV2 in vitro to recall human multi-epitope, functional, and cytotoxic SARS-CoV-2 S- and N-specific T-cell responses that are unaffected by VOC mutations and cross-reactive with SARS-CoV-1 and, to a lesser extent, MERS epitopes. Overall, these findings provide a framework for a pan-sarbecovirus vaccine.
Learning Two layer Networks with Multinomial Activation and High Thresholds. (2019)

Giving provable guarantees for learning neural networks is a core challenge of machine learning theory. Most prior work gives parameter recovery guarantees for one hidden layer networks. In this work we study a two layer network where the top node instead of a sum (one layer) is a well-behaved multivariate polynomial in all its inputs. We show that if the thresholds (biases) of the first layer neurons are higher than $\Omega(\sqrt{\log d})$ for $d$ being the input dimension, then the weights are learnable under the gaussian input. Furthermore even for lower thresholds, we can learn the lowest layer using polynomial sample complexity although exponential time. As an application of our results, we give a polynomial time algorithm for learning an intersection of halfspaces that are $\Omega(\sqrt{\log d})$ far from the origin for gaussian input distribution. Finally for deep networks with depth larger than two, assuming the layers two onwards can be expressed as a polynomial by simply using the taylor series, we can learn the lowest layer under the conditions required by our assumptions.
An Improved Partial Haar Dual Adaptive Filter For Sparse Echo Cancellation (2007)

This paper proposes the use of a peak tendency estimator (PTE) based on Dezert Smarandache Theory (DSmT) and fuzzy inference to overcome two inherent limitations of a recently proposed partial Haar dual adaptive filter (PHDAF) for sparse echo cancellation.
Placement of a wire mesh prosthesis in the external urinary sphincter of men with spinal cord injuries. (1993)

The authors report their experience with an intraurethral prosthetic stent as an alternative treatment for detrusor-external urethral sphincter dyssynergia (DESD). A sphincter prosthesis was inserted into the membranous urethra of 25 men with spinal cord injuries, DESD, and elevated voiding pressure. Bladder voiding pressure decreased from 87 cm H2O +/- 23 to 27 cm H2O +/- 11 in 12 months (P < .001). There was a significant decrease in residual urine volume 12 months after prosthesis placement, from 122 mL +/- 77 to 33 mL +/- 19 (P < .01); bladder capacity remained relatively unchanged, from 174 mL +/- 84 to 230 mL +/- 92 (P < .57). No deleterious effects were seen in renal or erectile function. Migration of three prostheses occurred 1 day to 6 weeks after insertion. One additional complication, pyelonephritis, occurred in a patient with preexisting vesicoureteral reflux, necessitating reimplantation of bilateral ureters. The intraurethral wire mesh prosthesis, with its simplicity of placement and minimal associated morbidity, offers a potential alternative to external sphincterotomy.
iPSC-Derived Ovarian Tissue Restores Ovarian Function in Subfertile Mice and After Gonadotoxic Chemotherapy (2019)

Abstract Many reproductive age women with cancer who receive chemotherapy are exposed to gonadotoxic agents and risk diminished ovarian reserve, sterility, and premature menopause. Previously, we reported the derivation of steroidogenic ovarian cells from induced pluripotent and embryonic stem cells. Derived cells not only produced reproductive hormones, but also displayed markers of ovarian tissue and primordial gametes. Here, we describe that human follicular fluid (HFF), when added to our stem cell differentiation system, enhances the steroidogenic potential of differentiating stem cells and increases the subpopulation of cells that express the ovarian and germ cell markers GJA1 and ZP1, respectively. More importantly, using an in vivo model of chemotherapy-induced premature ovarian insufficiency in subfertile nude mice, we demonstrate that orthotopic implantation of these derived cells restores ovarian hormone synthesis and produces functional stem cell-derived oocytes. Additionally, these cells also ameliorate subfertility in nude mice, as demonstrated by the delivery of multiple litters of healthy pups from stem cell-derived oocytes. Collectively, these data support the hypothesis that stem cell-derived steroidogenic ovarian tissue could be used to promote neo-gametogenesis and treat the endocrinologic and reproductive sequelae of premature ovarian insufficiency. One Sentence Summary We show that orthotopic injection of sorted, differentiated iPSCs in ovaries of subfertile mice restores reproductive hormone synthesis and fertility.