gebhart/patrepeval huggingface dataset:
Molecular biomarkers in the context of focal therapy for prostate cancer: recommendations of a Delphi Consensus from the Focal Therapy Society (2021)

The present study detailed an initial consensus on the use of MB in FT for PCa. This is until evidence becomes available on the subject.
ChemInform Abstract: Inhibitors of Acyl‐CoA: Cholesterol O‐Acyltransferase. Synthesis and Pharmacological Activity of (.+‐.)‐2‐Dodecyl‐α‐phenyl‐N‐(2,4,6‐ trimethoxyphenyl)‐2H‐tetrazole‐5‐acetamide and Structurally Related Tetrazole Amide Derivatives. (1996)

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.
Computational approaches to molecular recognition (1997)

Recent advances in the computation of free energies have facilitated the understanding of host-guest and protein-ligand recognition. Rigorous perturbation methods have been assessed and expanded, and more approximate techniques have been developed that allow faster treatment of diverse systems.
Food size and cGMP affects feeding behaviour in Pristionchus pacificus (2011)

Keywords: Locomotory BehaviorDependent Protein KinaseReversal RateLocomotion PatterncGMP Dependent Protein Kinase
Measurement of inclusiveπ0production in the charged-current interactions of neutrinos in a 1.3-GeV wide band beam (2011)

In this paper, we report on the measurement of the rate of inclusive ${\ensuremath{\pi}}^{0}$ production induced by charged-current neutrino interactions in a ${\mathrm{C}}_{8}{\mathrm{H}}_{8}$ target at a mean energy of 1.3 GeV in the K2K near detector. Out of a sample of 11 606 charged-current neutrino interactions, we select 479 ${\ensuremath{\pi}}^{0}$ events with two reconstructed photons. We find that the cross section for the inclusive ${\ensuremath{\pi}}^{0}$ production relative to the charged-current quasielastic cross section is $\frac{{\ensuremath{\sigma}}_{\mathrm{CC}{\ensuremath{\pi}}^{0}}}{{\ensuremath{\sigma}}_{\mathrm{CCQE}}}=0.426\ifmmode\pm\else\textpm\fi{}0.032\text{ }(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.035\text{ }(\mathrm{syst})$. The energy-dependent cross section ratio is also measured. The results are consistent with previous experiments for exclusive channels on different targets.
Cytometric Detection and Quantitation of Cell-Cell Electrofusion Products (1995)

Cell-cell electrofusion (CCE) is a process that involves forcing cells into close juxtaposition and then inducing fusion by delivering electric pulses to the cells. CCE has proven to have many practical applications. It has been used for monoclonal antibody (MAb) production (,), hybridoma production (, , ), and to transfer membrane-surface markers (). Many other applications are described in this volume. In addition, the study of membrane fusion mechanisms has been the focus of some researchers (, , , , , ). Electrofusion techniques seldom result in 100% yield between fusion partners. Therefore, a major aspect of CCE applications is the ability to detect and quantitate fusion products.
Compressed sensing based channel estimation and impulsive noise cancelation in underwater acoustic OFDM systems (2016)

Impulsive noise occurs frequently in underwater acoustic (UA) channels and can significantly degrade the performance of UA orthogonal frequency-division multiplexing (OFDM) systems. In this paper, we propose a novel compressed sensing based algorithm for joint channel estimation and impulsive noise cancelation in UA OFDM systems. The proposed algorithm jointly estimates the channel impulse response and the impulsive noise by utilizing the pilot subcarriers. The estimated impulsive noise is then converted to the time domain and removed from the received signals. The proposed algorithm is applied to process the data collected during the UA communication experiment conducted in December 2015 in the estuary of the Swan River, Western Australia. The results show that the proposed approach improves the performance of both channel estimation and impulsive noise mitigation.
A Dzyaloshinskii-Moriya Anisotropy in Nanomagnets with in-plane Magnetization (2015)

We report on a new source of in-plane anisotropy in nanomagnets due to the presence of Dzyaloshinskii-Moriya interaction (DMI). This anisotropy depends on the shape of the magnet, and is orthogonal to the demagnetization shape anisotropy. This effect originates from the DMI energy reduction due to an out-of-plane tilt of the spins at edges oriented perpendicular to the magnetization. Our investigation combining experimental, numerical and analytical results demonstrate that this energy reduction can compensate the demagnetization shape anisotropy energy in magnets of elongated shape, provided that their volumes is small enough and thus that their magnetization is quasi-uniform.
Frequency tunability of solid-core photonic crystal fibers filled with nanoparticle-doped liquid crystals (2009)

We infiltrate liquid crystals doped with BaTiO3 nanoparticles in a photonic crystal fiber and compare the measured transmission spectrum with the one achieved without dopant. New interesting features, such as frequency modulation response of the device and a transmission spectrum with tunable attenuation on the short wavelength side of the widest bandgap, suggest a potential application of this device as a tunable all-in-fiber gain equalization filter with an adjustable slope. The tunability of the device is achieved by varying the amplitude and the frequency of the applied external electric field. The threshold voltage for doped and undoped liquid crystals in a silica capillary and in a glass cell are also measured as a function of the frequency of the external electric field and the achieved results are compared.
Morphological Indicator for Directed Evolution of Euglena gracilis with a High Heavy Metal Removal Efficiency (2021)

In the past few decades, microalgae-based bioremediation methods for treating heavy metal (HM)-polluted wastewater have attracted much attention by virtue of their environment friendliness, cost efficiency, and sustainability. However, their HM removal efficiency is far from practical use. Directed evolution is expected to be effective for developing microalgae with a much higher HM removal efficiency, but there is no non-invasive or label-free indicator to identify them. Here, we present an intelligent cellular morphological indicator for identifying the HM removal efficiency of Euglena gracilis in a non-invasive and label-free manner. Specifically, we show a strong monotonic correlation (Spearman’s ρ = −0.82, P = 2.1 × 10–5) between a morphological meta-feature recognized via our machine learning algorithms and the Cu2+ removal efficiency of 19 E. gracilis clones. Our findings firmly suggest that the morphology of E. gracilis cells can serve as an effective HM removal efficiency indicator and hence have great potential, when combined with a high-throughput image-activated cell sorter, for directed-evolution-based development of E. gracilis with an extremely high HM removal efficiency for practical wastewater treatment worldwide.
Testing integrability with a single bit of quantum information (2003)

We show that deterministic quantum computing with a single bit can determine whether the classical limit of a quantum system is chaotic or integrable using $O(N)$ physical resources, where N is the dimension of the Hilbert space of the system under study. This is a square-root improvement over all known classical procedures. Our study relies strictly on the random matrix conjecture. We also present numerical results for the nonlinear kicked top.
Trichosporon asahii infection of a dialysis PTFE arteriovenous graft (2004)

Trichosporon species are the causative agents of superficial skin infections, such as white piedra. Immunocompromised hosts, particularly those with underlying hematological malignancy, are at risk of developing invasive infection, which usually progresses to disseminated life-threatening disease. Peritonitis caused by Trichosporon has been described in end-stage renal disease patients treated with continuous ambulatory peritoneal dialysis. Here, we report on a Trichosporon infection of an arteriovenous graft in a patient on chronic hemodialysis. The infection was successfully treated with fluconazole and total surgical resection of the graft.
Antimicrobial Photodynamic Therapy to Control Clinically Relevant Biofilm Infections (2018)

Biofilm describes a microbially-derived sessile community in which microbial cells are firmly attached to the substratum and embedded in extracellular polymeric matrix. Microbial biofilms account for up to 80% of all bacterial and fungal infections in humans. Biofilm-associated pathogens are particularly resistant to antibiotic treatment, and thus novel antibiofilm approaches needed to be developed. Antimicrobial Photodynamic therapy (aPDT) had been recently proposed to combat clinically relevant biofilms such as dental biofilms, ventilator associated pneumonia, chronic wound infections, oral candidiasis, and chronic rhinosinusitis. aPDT uses non-toxic dyes called photosensitizers (PS), which can be excited by harmless visible light to produce reactive oxygen species (ROS). aPDT is a multi-stage process including topical PS administration, light irradiation, and interaction of the excited state with ambient oxygen. Numerous <i>in vitro</i> and <i>in vivo</i> aPDT studies have demonstrated biofilm-eradication or substantial reduction. ROS are produced upon photo-activation and attack adjacent targets, including proteins, lipids, and nucleic acids present within the biofilm matrix, on the cell surface and inside the microbial cells. Damage to non-specific targets leads to the destruction of both planktonic cells and biofilms. The review aims to summarize the progress of aPDT in destroying biofilms and the mechanisms mediated by ROS. Finally, a brief section provides suggestions for future research.
New Experimental Tool for Enhanced Fiber Mode Analysis (2013)

S2 imaging and CFT mode analysis are combined and simultaneously performed. This unique tool provides fully resolved modal fields and accurate mode coefficients for a wide range of mode mixtures guided in an optical fiber. © OSA 2013.
S3–02–06: Associations between medication usage and the incidence of Alzheimer disease: Effects observed for cardiovascular and immunomodulatory medications (2006)

Multiple studies have examined the influence of individual pharmaceutical agents on the incidence or progression of AD, however there is no comprehensive database describing the influence of current medications on the incidence or progression of AD. Identify pharmaceutical agents that modify the incidence of Alzheimer's disease (AD). We analyzed the Veterans Affairs (VA) pharmaceutical database, which contains information on 8,000,000 individuals. We excluded individuals under 60 yrs and individuals who had a pre–existing diagnosis of senile dementia of the Alzheimer type, ICD9 331.0, here after referred to as SDAT. Next, we screened medication classes within the database. Medicines in the VA formulary are divided into 300 classes, each containing up to 12 medications. The incidence of SDAT was determined for each class, and the odd ratios were risk adjusted for age and compared to other major medication classes to statistically isolate primary drug effects of that class. Risk adjustments were based upon multivariate logistic regression. Ongoing studies will complete the multivariate analysis including assessment of co–variate medication usage and co–morbid diagnoses. We are currently repeating the study examining individual medications in addition to medication classes. Cardiovascular medications showed a striking association with SDAT. 75% of the medication classes in the cardiovascular disease category are associated with an elevated incidence of SDAT. For instance, the medication class CV400, ‘Antihypertensive Combinations’, exhibited an odds ratio of 1.9 with confidence intervals of 1.1 – 3.3 (p<0.001). The cardiovascular medications group exhibited the most frequent association with AD compared to the other groups of medications. Immunomodulatory agents also exhibited a significant influence on the incidence of AD. Vaccines for influenza (FluVax) or pneumococcus (PneumoVax) exhibited lower odds ratios (FluVax: OR 0.41, CI 0.332–0.505, p<0.001, PneumoVax OR 0.395, CI 0.288–0.505, p<0.001). In contrast, a class of medications containing cromolyn sodium (RE109) exhibited an increased odds ratio (OR 1.47, CI 1.24 – 1.76. p<0.001). These results raise the possibility that selected medications might modify the incidence of AD either due to a modifying action of the medication or the associated disease process on the pathophysiology of AD.
AN OBSERVATIONAL STUDY DEMONSTARTING THE MEASUREMENT, CHARACTERIZATION AND VALIDATION OF EXPRESSIONS OF CALPROTECTIN IN HUMAN SWEAT THROUGH A SWEAT WEARABLE (2023)

Abstract BACKGROUND Inflammatory bowel diseases (IBD) comprising Crohn’s disease (CD) and ulcerative colitis (UC) are typically characterized by chronic episodes of inflammation within and through the gastrointestinal (GI) tract. In many inflammatory conditions including IBD, Calprotectin (CP) is well-studied (systemic and fecal) and employed by clinicians due to assay stability and low cost to effectively guide diagnostic and therapeutic decisions. While, accessing fecal CP is non-invasive, there is significant resistance to continuous fecal CP testing from patient-use and patient enablement aspects due to the challenges is sample collection, hence there is a current unmet need to access CP in a completely non-invasive manner. METHODS The sweat sensor device and reference ELISA was used to investigate and quantify CP levels in sweat. The immunoassay on the sweat sensor was developed by immobilizing specific capture probe antibody to capture CP in sweat. The sensor response was measured using impedance spectroscopy. Sweat samples from seven healthy and one IBD subject were collected and correlation analysis between the sweat sensor device and ELISA was performed to evaluate CP levels in sweat. RESULTS The sweat sensor device demonstrated a wide dynamic range of 0.1- 10 μg/mL with a limit of detection of 0.1 μg/mL. The sensor was also specific to CP and demonstrated negligible to no response for non-specific inflammatory markers such as C-reactive protein, interleukin-6. Excellent correlation was achieved between ELISA and the sweat sensor device with Pearson’s r&amp;gt;0.95. Human subject studies demonstrated that elevated basal levels in IBD subject (500 ng/mL) as compared to healthy cohort (~ 350 ng/mL). Further, 3 times increase in CP levels was observed due to flare-up in the IBD subject with a mean concentration ~1300 ng/mL as compared to the basal levels. CONCLUSION This work is the first demonstration of CP in sweat. The pre-clinical results of elevated CP levels will be of significant interest to clinicians as it provides a non-invasive and non-intrusive tracking flare-ups in IBD patients and can aid in better management of the disease.
Short Article The IGF-1/PI3K/Akt Pathway Prevents Expression of Muscle Atrophy-Induced Ubiquitin Ligases by Inhibiting FOXO Transcription Factors (2004)

Summary membrane phospholipid phosphatidylinositol-4,5-bis- phosphate to phosphatidylinositol-3,4,5-trisphosphate, Skeletalmusclesizedependsuponadynamicbalance creating a lipid binding site on the cell membrane forbetween anabolic (or hypertrophic) and catabolic (or a serine/threonine kinase called Akt (or PKB—protein atrophic) processes. Previously, no link between the kinase B). The subsequent translocation of Akt to themolecular mediators of atrophy and hypertrophy had membrane facilitates its phosphorylation and activation been reported. We demonstrate a hierarchy between by the kinase PDK-1 (Cantley, 2002; Datta et al., 1999;the signals which mediate hypertrophy and those Vivanco and Sawyers, 2002). Cell growth and survival which mediate atrophy: the IGF-1/PI3K/Akt pathway, inavarietyoftissuesandcelltypesinresponsetoIGF-1,which has been shown to induce hypertrophy, pre- insulin, and other growth factors is critically mediated ventsinductionofrequisiteatrophymediators,namely by Akt (Datta et al., 1999; Vivanco and Sawyers, 2002).the muscle-specific ubiquitin ligases MAFbx and
Metallo‐Rotaxanes and Catenanes as Redox Switches: Towards Molecular Machines and Motors (2001)

Introduction Generalities Regarding Machines and Motors Proteins Undergoing Folding–Defolding Processes Biological Molecular Motors Previously Described Synthetic Systems based on Purely Organic Components Motion in Transition Metal-based Molecules Rotaxanes Containing Transition Metals: From Electronic to Molecular Motion Photoinduced Intramolecular Electron Transfer Within Porphyrinic Rotaxanes Lateral Translation of a Ring on the Molecular String on which it is Threaded: Electrochemically-driven Motion Towards Rotary Motors: Pirouetting of a Two-coordinate Ring on its Thread Electrochemical Behavior of Chemically Isolated 16(4)+ and 16(5)2+ Electrochemically Driven Ring Gliding Motion in Catenanes A Twin-geometry Catenane A Triplet-configuration Copper Catenane Conclusion and Prospects
HPV-targeted tumor-infiltrating lymphocytes for cervical cancer. (2014)

LBA3008 Background: Adoptive T-cell therapy (ACT) is a promising cancer treatment modality with potentially broad application. It is not known if ACT can mediate regression of carcinomas, the most common solid tumors in humans. We studied carcinoma of the uterine cervix, a virally induced malignancy that constitutively expresses the HPV E6 and E7 oncoproteins, as a model cancer to test if ACT can mediate regression of an epithelial malignancy. Methods: We initiated a clinical trial to treat metastatic HPV+ cancers with tumor-infiltrating lymphocytes (TIL) selected for HPV E6- and E7-reactivity (HPV-TIL). Patients from the cervical cancer cohort are reported here. HPV-TIL infusion was preceded by non-myeloablative conditioning and followed by high-dose bolus aldesleukin. HPV-reactivity was assessed by ELISPOT, IFN-gamma production, and CD137 expression assays. Results: Nine patients were treated on the study. They received a median of 81 x 109 T cells (range 33 to 159 x 109) as a single infusion. The infused cells possessed reactivity against high-risk HPV E6 and/or E7 in 6/8 patients. The two patients with no HPV reactivity did not respond to treatment. 3/6 patients with HPV reactivity demonstrated objective tumor responses by RECIST (1 PR and 2 CR). One patient had a 39% best response. Two patients with widespread metastases had complete tumor responses that are ongoing 18 and 11 months after treatment. One patient with a complete response had a chemotherapy-refractory HPV-16+ squamous cell carcinoma and the other a chemoradiation-refractory HPV-18+ adenocarcinoma. Both patients demonstrated prolonged repopulation with HPV-reactive T cells following treatment. Increased frequencies of HPV-specific T cells were detectable after 13 months in one patient and 6 months in the other. Two patients with HPV-reactive TIL that did not respond to treatment did not display repopulation with HPV-reactive T cells. Conclusions: HPV-TIL can mediate durable, complete regression of metastatic cervical cancer. Continued investigation of HPV-TIL for cervical cancer, and possibly other HPV+ malignancies, is warranted. Cellular therapy can mediate complete regression of an epithelial malignancy. Clinical trial information: NCT01585428.
Pulmonary Function Changes After Various Anterior Approaches in the Treatment of Adolescent Idiopathic Scoliosis (2009)

Slight declines in pulmonary function at 2-year follow-up were noted in both the thoracotomy and thoracoscopic groups, but to a significantly greater extent in those with an open thoracotomy. Significantly greater impairment in pulmonary function was seen in thoracoscopic patients who underwent thoracoplasty, whereas those without thoracoplasty either had no significant declines at 2 years or experienced slight but significant improvement. No significant diminishment was noted for the thoracoabdominal approach, despite disruption of the diaphragm.
Volume estimation of tonsil phantoms using an oral camera with 3D imaging (2016)

Three-dimensional (3D) visualization of oral cavity and oropharyngeal anatomy may play an important role in the evaluation for obstructive sleep apnea (OSA). Although computed tomography (CT) and magnetic resonance (MRI) imaging are capable of providing 3D anatomical descriptions, this type of technology is not readily available in a clinic setting. Current imaging of the oropharynx is performed using a light source and tongue depressors. For better assessment of the inferior pole of the tonsils and tongue base flexible laryngoscopes are required which only provide a two dimensional (2D) rendering. As a result, clinical diagnosis is generally subjective in tonsillar hypertrophy where current physical examination has limitations. In this report, we designed a hand held portable oral camera with 3D imaging capability to reconstruct the anatomy of the oropharynx in tonsillar hypertrophy where the tonsils get enlarged and can lead to increased airway resistance. We were able to precisely reconstruct the 3D shape of the tonsils and from that estimate airway obstruction percentage and volume of the tonsils in 3D printed realistic models. Our results correlate well with Brodsky's classification of tonsillar hypertrophy as well as intraoperative volume estimations.
Effect of polymer architecture on self-diffusion of LC polymers (1999)

Two LC side-group poly(methacrylates) were synthesized, and their melt dynamics were compared with each other and a third, main-chain side-group combined LC polymer. A new route was developed for the synthesis of the poly(methacrylate) polymers which readily converts relatively inexpensive perdeuteromethyl methacrylate to other methacrylate monomers. Self-diffusion data was obtained through the use of forward recoil spectrometry, while modulus and viscosity data were measured using rotational rheometers in oscillatory shear. Diffusion coefficients and complex viscosity were compared to previous experiments on liquid crystal polymers of similar architecture to determine the effect of side-group interdigitation and chain packing on center of mass movement. The decyl terminated LC side-group polymer possessed an interdigitated smectic phase and a sharp discontinuity in the self-diffusion behavior at the clearing transition. In contrast, the self-diffusion behavior of the methyl terminated LC side-group polymer, which possessed head-to-head side-group packing, was seemingly unaffected by the smectic–nematic and nematic–isotropic phase transitions. The self-diffusion coefficients of both polymers were relatively insensitive to the apparent glass transition. The presence of moderately fast sub-Tg chain motion was supported by rheological measurements that provided further evidence of considerable molecular motion below Tg. The complex phase behavior of the combined main-chain side-group polymer heavily influenced both the self-diffusion and rheological behavior. Differences between the self-diffusion and viscosity data of the main-chain side-group polymer could be interpreted in terms of the defect structure. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 405–414, 1999