gebhart/patrepeval huggingface dataset:
Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain (2022)

Doublecortin (DCX) is a microtubule (MT)-associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX-MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-electron microscopy, and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its tail, our study shows that lattice-driven self-assembly is an important property of DCX.
An Enhanced Understanding of Culture-Negative Periprosthetic Joint Infection with Next-Generation Sequencing: A Multicenter Study. (2022)

Diagnostic Level II . See Instructions for Authors for a complete description of levels of evidence.
Novel chiral liquid crystals derived from (R)-2-(4-hydroxyphenoxy)propan-1-ol (1993)

The thermotropic liquid-crystalline behaviour of a number of (R)- and (R,S)-2-(4-substituted-phenoxy)-1-alkoxy propanes has been examined and related to changes in the nature of the mesogenic core and the terminal alkoxy substituent. Compounds containing a 4′-pentylbiphenyl-4-carbonyloxy core were generally found to display smectic A and the more ordered crystal B mesophases; in contrast the 4-(4-trans-pentylcyclohexyl)benzoyloxy-derived series showed chiral nematic and Blue phases in addition to the smectic A and crystal B phases. Furthermore, the high optical purity of these materials was demonstrated by use of 1H NMR and chiral shift reagent techniques, and confirms the stability of the chiral centre towards racemization.
In-plane wavelength multiplexing of fibre Bragg gratings in a multicore optical fibre (2019)

We present separation of fibre Bragg grating wavelength reflections in a multicore fibre with an even peak wavelength distance between reflections in the multiple cores of a single cross-section plane. The inscription is achieved simultaneously in all cores by applying a bend in the fibre, and thus inducing a different variation of the effective refractive index in each core. Such method for wavelength multiplexing would enable the interrogation of multiple sensors signals delivered by a single channel, e.g., without the need of a fanout device or a multichannel spectrometer.
Supplementary Table 3 from Proteomic Profiling Identifies Dysregulated Pathways in Small Cell Lung Cancer and Novel Therapeutic Targets Including PARP1 (2023)

&lt;p&gt;PDF file, 83K, Proteins with ≥1.2-fold differential expression between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC).&lt;/p&gt;
A unifying fractional wave equation for compressional and shear waves (2010)

This study has been motivated by the observed difference in the range of the power-law attenuation exponent for compressional and shear waves. Usually compressional attenuation increases with frequency to a power between 1 and 2, while shear wave attenuation often is described with powers less than 1. Another motivation is the apparent lack of partial differential equations with desirable properties such as causality that describe such wave propagation. Starting with a constitutive equation which is a generalized Hooke's law with a loss term containing a fractional derivative, one can derive a causal fractional wave equation previously given by Caputo [Geophys J. R. Astron. Soc. 13, 529-539 (1967)] and Wismer [J. Acoust. Soc. Am. 120, 3493-3502 (2006)]. In the low omegatau (low-frequency) case, this equation has an attenuation with a power-law in the range from 1 to 2. This is consistent with, e.g., attenuation in tissue. In the often neglected high omegatau (high-frequency) case, it describes attenuation with a power-law between 0 and 1, consistent with what is observed in, e.g., dynamic elastography. Thus a unifying wave equation derived properly from constitutive equations can describe both cases.
Acetabular Reconstruction Using Bipolar Endoprosthesis and Bone Grafting in Patients With Severe Bone Deficiency (1995)

Eighty-one patients who had hip reconstruction with bone grafting and bipolar endoprosthesis for severe acetabular deficiency were reviewed retrospectively at 3 to 8 years postoperatively. Failed total hip arthroplasty was the most common indication for operation. Bone grafts were fixed bone blocks, morselized cancellous bone, and wafer-type grafts used singly or in combination. The average Harris hip rating score was 49.9 points preoperatively, 81.4 points at 1 year, and 70.8 points at latest followup examination. The 35 unsuccessful procedures included 25 reoperations for implant removal (resection arthroplasty or revision) and 10 cases pending revision. At latest followup examination, 54.7% of patients considered themselves improved and 62.7% had no or mild pain. Eighty-five percent of cases had radiographic evidence of component migration that was superior and medial in direction. Overall probability of implant survival was 96% at 1 year, but only 47% at 6.5 years postoperatively. Because of the high failure rate, this procedure has a limited role in hip reconstruction, but may be a reasonable part of a staged reconstruction for patients with massive bone loss or in certain revision cases where instability is a concern.
ChemInform Abstract: Aluminum Dichloride and Dibromide. Preparation, Spectroscopic (Including Matrix Isolation) Study, Reactions, and Role (Together with Alkyl(aryl)aluminum Monohalides) in the Preparation of Organoaluminum Compounds. (1988)

Abstract The paramagnetic aluminum dichloride and dibromide associated in the condensed state are prepared and isolated for the first time by the reaction of Al metal with AlCl 3 or AlBr 3 , Al2(iBu)4 with HCl, and Al atoms with Cl2 using matrix isolation techniques.
Pulsetrain-burst mode, ultrafast-laser interactions with 3D viable cell cultures as a model for soft biological tissues (2013)

A 3D living-cell culture in hydrogel has been developed as a standardized low-tensile-strength tissue proxy for study of ultrafast, pulsetrain-burst laser-tissue interactions. The hydrogel is permeable to fluorescent biomarkers and optically transparent, allowing viable and necrotic cells to be imaged in 3D by confocal microscopy. Good cell-viability allowed us to distinguish between typical cell mortality and delayed subcellular tissue damage (e.g., apoptosis and DNA repair complex formation), caused by laser irradiation. The range of necrosis depended on laser intensity, but not on pulsetrain-burst duration. DNA double-strand breaks were quantified, giving a preliminary upper limit for genetic damage following laser treatment.
IEEE Access Special Section Editorial: Advanced Energy Conversion Systems Based on Multi-Port Electrical Machines (2021)

Over the last decade, with the merits of high efficiency, compactness, and flexibility, energy conversion systems based on multiple-electrical-port and multiple-mechanicalport electrical machines have attracted widespread attention from both academia and industry. This concept has been adopted in many industrial applications, such as wind power generation, ship shaft power generation, ship electric propulsion, electric vehicles, rail transportation, more/all electric aircrafts, and ac/dc microgrids. Due to the ever-increasing demand for highly reliable and cost-effective energy conversion systems, advanced machine/converter topologies, modeling approaches, control strategies, and reliability, evaluations of multi-port electrical machines and drive systems are in great need.
Stable High‐Conductivity Ethylenedioxythiophene Polymers via Borane‐Adduct Doping (2022)

Abstract Efficient doping of polymer semiconductors is required for high conductivity and efficient thermoelectric performance. Lewis acids, e.g., B(C 6 F 5 ) 3 , have been widely employed as dopants, but the mechanism is not fully understood. 1:1 “Wheland type” or zwitterionic complexes of B(C 6 F 5 ) 3 are created with small conjugated molecules 3,6‐bis(5‐(7‐(5‐methylthiophen‐2‐yl)‐2,3‐dihydrothieno[3,4‐b][1,4]dioxin‐5‐yl)thiophen‐2‐yl)‐2,5‐dioctyl‐2,5‐dihydropyrrolo[3,4‐c]pyrrole‐1,4‐dione [oligo_DPP(EDOT) 2 ] and 3,6‐bis(5''‐methyl‐[2,2':5',2''‐terthiophen]‐5‐yl)‐2,5‐dioctyl‐2,5‐dihydropyrrolo[3,4‐c]pyrrole‐1,4‐dione [oligo_DPP(Th) 2 ]. Using a wide variety of experimental and computational approaches, the doping ability of these Wheland Complexes with B(C 6 F 5 ) 3 are characterized for five novel diketopyrrolopyrrole‐ethylenedioxythiophene (DPP‐EDOT)‐based conjugated polymers. The electrical properties are a strong function of the specific conjugated molecule constituting the adduct, rather than acidic protons generated via hydrolysis of B(C 6 F 5 ) 3 , serving as the oxidant. It is highly probable that certain repeat units/segments form adduct structures in p ‐type conjugated polymers which act as intermediates for conjugated polymer doping. Electronic and optical properties are consistent with the increase in hole‐donating ability of polymers with their cumulative donor strengths. The doped film of polymer (DPP(EDOT) 2 ‐(EDOT) 2 ) exhibits exceptionally good thermal and air‐storage stability. The highest conductivities, ≈300 and ≈200 S cm −1 , are achieved for DPP(EDOT) 2 ‐(EDOT) 2 doped with B(C 6 F 5 ) 3 and its Wheland complexes.
Correlations Between Changes in Gait and in Clinical Status After Knee Arthroplasty (1981)

Twenty-six knee arthroplastics in 22 subjects were studied clinically and in a gait laboratory before and on one or more occasions after surgery. The purpose was to identify changes in gait characteristics and relate them to changes in the clinical situation of the patients. The gait patterns of the patients changed following surgery mainly with respect to their time-distance characteristics; stride length, cadence, time of swing, and time of support. Positive correlations were noted between these gait changes and the patient's pain, his limp, and his walking distance. It is concluded that the information obtained in sophisticated gait laboratory is of limited value to the surgeon in his clinical assessment.
Halogenation dictates architectures and properties of amyloid peptides (2019)

Besides pathological roles in many diseases, e.g., Alzheimer's, Parkinson's, Creutzfeldt-Jakob, and Huntington's, amyloid peptide architectures have found many other non-biological applications such as forming highly ordered nanomaterials. Together with their biocompatibility and the ease of production, amyloidogenic peptides show a very versatile polymorphic behavior yielding a broad range of hierarchical structures, such as tapes, ribbons, fibers, nanoparticles, and nanotubes. Subtle variations in the experimental conditions, peptide sequence or its chemical functionalization may impact the self-assembly pathway and, consequently, the resulting nanostructures. Here we report that depending on the number, position, and nature of the halogen atoms introduced into either one or both phenylalanine benzene rings of the amyloid peptide-derived core-sequences such as DFNKF (H 2 N-Asp-Phe-Asn-Lys-Phe-COOH) and KLVFF (H 2 N-Lys-Leu-Val-Phe-Phe-COOH), different architectures and properties are obtained in a controlled manner
Hernia de Amyand con apendicitis aguda y tumor carcinoide (2020)

Introduccion: La hernia de Amyand fue descrita en 1735 por el cirujano Claudius Amyand (1680-1740) como 
la presencia de un apendice cecal contenido dentro del saco herniario con incidencia del 1 %. Su coexistencia con la 
presencia de un tumor carcinoide del apendice dentro de un saco herniario inguinal es una entidad aun mas rara, por 
lo que se presenta caso. 
Caso clinico: Hombre de 71 anos con una hernia inguinal complicada y cuyo diagnostico de apendicitis se realizo 
en pabellon despues de abrir el saco herniario y de un tumor carcinoide en el estudio histopatologico. 
Discusion: El estudio de imagenes, en particular la tomografia axial computarizada (TAC), ha sido utilizado para 
plantear el diagnostico de hernia de Amyand. El tratamiento recomendado es la apendicectomia y la reparacion primaria 
de la hernia en el mismo tiempo operatorio. No debe utilizarse protesis por el riesgo de infeccion y fistula del 
munon apendicular. Por otra parte, la posibilidad de encontrar en la biopsia apendicular un tumor carcinoide es rara. Es 
necesario su exeresis. Dada la escasa literatura, consideramos que el tratamiento optimo para la patologia en cuestion, 
en presencia de apendicitis, es la apendicectomia y la reparacion anatomica y, en un segundo momento, la colocacion 
de la malla. Al enfrentarse a un tumor carcinoide, sugerimos como tratamiento estandar la apendicectomia en paciente 
mayor de 60 anos
Improved OT Extension for Transferring Short Secrets. (2013)

We propose an optimization and generalization of OT extension of Ishai et al. of Crypto 2003. For computational security parameter k, our OT extension for short secrets offers O(log k) factor performance improvement in communication and computation, compared to prior work. In concrete terms, for today’s security parameters, this means approx. factor 2-3 improvement. This results in corresponding improvements in applications relying on such OT. In particular, for two-party semi-honest SFE, this results in O(log k) factor improvement in communication over state of the art Yao Garbled Circuit, and has the same asymptotic complexity as the recent multi-round construction of Kolesnikov and Kumaresan of SCN 2012. For multi-party semi-honest SFE, where their construction is inapplicable, our construction implies O(log k) factor communication and computation improvement over best previous constructions. As with our OT extension, for today’s security parameters, this means approximately factor 2 improvement in semi-honest multi-party SFE. Our building block of independent interest is a novel IKNP-based framework for 1-out-of-n OT extension, which offers O(logn) factor performance improvement over previous work (for n ≤ k), and concrete factor improvement of up to 5 for today’s security parameters (n=k=128). Our protocol is the first practical OT with communication/computation cost sublinear in the security parameter (prior sublinear constructions Ishai et al. [15, 16] are not efficient in concrete terms).
At Speed Testing Challenges and Solutions for 56Gbps and 112Gbps PAM4 SerDes (2020)

Margining Test with either internal or external loopback has become a popular Design for Test (DfT) feature in high-speed SerDes. These SerDes DfT-derived results are becoming more unreliable because SerDes devices are pushing the limits of process variability. In addition, implementing DfT at the high-speed side of a device introduces the age-old problem of performance degradation due to the added circuitry. Given that many of these devices have very little performance margin, it is problematic to cause even a small reduction in performance. This is becoming more apparent with new Ethernet SerDes pushing the 100Gbps data rate. As with most new technology, more efficient and targeted DfT and BIST will emerge once the failure mechanisms and process dependencies of the devices are better known. For now, functional and parametric testing for these SerDes is generally required to make end-users comfortable that these devices are performing to spec and relying on off chip features implementation. Additionally, new DfT techniques and new metrics are being introduced to ensure manufacturing of these products.
Isoflurane and Halothane Do Not Alter the Enhanced Afterload Sensitivity of Left Ventricular Relaxation in Dogs with Pacing-induced Cardiomyopathy (1997)

The results indicate that isoflurane and halothane do not alter the afterload dependence of LV relaxation in the normal and cardiomyopathic heart. The lack of effect of the volatile anesthetics is probably related to anesthetic-induced reductions in the resistance to LV ejection concomitant with simultaneous negative inotropic effects.
OT-1096: A first-in-class immunoactivating small molecule that targets the thioredoxin reductase/thioredoxin axis causes strong tumor growth inhibition by downregulating intratumoral tregs in a humanized TNBC-PDX model (2018)

Background: Triple-negative breast cancer is an aggressive subtype associated with poor prognosis and limited treatment options, and new effective medicines are needed. We have developed a novel class of SecTRAP- forming small molecules that lead to a change-of-function of thioredoxin reductase that is cytotoxic to cancer cells (Staffort et al. Sci Transl Med, 2018). However, the immunomodulatory effects of OT-1096 are unknown. This study examined the efficacy of OT-1096 in humanized CD34+ NSG mice bearing patient-derived TNBC xenografts and compared the efficacy of OT-1096 to pembrolizumab. Additionally, the immunoactivating effects of OT-1096 were analyzed. Methods: NSG mice, humanized with CD34+ stem cells from 3 different human donors were engrafted with TNBC invasive ductal carcinoma patient-derived xenografts. The mice were treated with OT-1096 (10mg/kg IV) tiwk and was compared to treatment with pembrolizumab (10mg/kg initial dose, thereafter 5mg/kg IP) biwk, single agent and in combination with OT-1096. Tumor volume was measured using calipers for 31 days and xenografts were analyzed with FACS to determine immune cell infiltration at day 41(sacrifice). Results: OT-1096 showed statistically significant tumor growth inhibition (TGI: 63%) when comparing treatments arms with all three donors combined. OT-1096 also presented improved tumor growth control compared to pembrolizumab. FACs analysis of xenografts showed OT-1096-treated tumors to have a lower fraction of Tregs within the TIL population as compared to controls. OT-1096 treatment was both safe and well tolerated. Conclusions: OT-1096 shows promising results in a humanized mouse TNBC PDX model with improved tumor growth inhibition compared to pembrolizumab. The results suggest that OT-1096 possesses both redox system modulation and beneficial immunomodulatory potential, and warrants further investigations of OT-1096 in TNBC and other malignancies. Legal entity responsible for the study: Oblique Therapeutics AB. Funding: Oblique Therapeutics AB. Disclosure: O. Orwar: Stock owner, board of directors, CEO: Oblique Therapeutics. I. Lowstedt, G. Willman, M. Davidsson: Full-time employee: Oblique Therapeutics. W. Stafford: Employee and shareholder: Oblique Therapeutics. C. Trkulja: Stock owner, board of directors, full-time employee: Oblique Therapeutics. All other authors have declared no conflicts of interest.
Intrawell stochastic resonance versus interwell stochastic resonance in underdamped bistable systems (2000)

We show that, for periodically driven noisy underdamped bistable systems, an intrawell stochastic resonance can exist, together with the conventional interwell stochastic resonance, resulting in a double maximum in the power spectral amplitude at the forcing frequency as a function of the noise intensity. The locations of the maxima correspond to matchings of deterministic and stochastic time scales in the system. In this paper we present experimental evidence of these phenomena and a phemonological nonadiabatic description in terms of a noise-controlled nonlinear dynamic resonance.
Opening of Tartrate Acetals Using Dialkylboron Bromide:  Evidence for Stereoselectivity Downstream from Ring Fission (2002)

Johnson-type acetals derived from dimethyl tartrate give, after opening with Me(2)BBr and cuprate displacement, secondary alcohols with high diastereoselectivity (>30:1). The mechanism proposed for the induction of diastereoselectivity is downstream from the ring fission. It implies a direct participation of the Lewis acid as a source of nucleophile and the stereospecific transformation of the resulting bromo acetal through an invertive and temperature-dependent process. The acetals are prepared by reaction of the desired aldehyde with dimethyl tartrate. Removal of the auxiliary is accomplished through SmI(2) reduction or by an addition-elimination protocol using methoxide.
Charge transport in a CoPt3 nanocrystal microwire (2004)

The electrical characteristics of single CoPt3 nanocrystal microwires formed by magnetic field-directed growth from colloidal solutions are presented. The wires comprise disordered assemblies of discrete nanocrystals, separated from each other by protective organic ligand shells. Electrical data indicate that the activated charge transport properties of the wires are determined by the nanocrystal charging energy, governed by the size and capacitance of the individual nanocrystals. Focused ion beam-assisted deposition of Pt metal at the wire-electrode junctions is employed to optimize the wire-electrode contacts, whilst maintaining the nanocrystal-dominated transport characteristics of these one-dimensional nanocrystal structures.
Forward Vaccinology: CTL Targeting Based upon Physical Detection of HLA-Bound Peptides (2014)

Vaccine-elicited cytotoxic T lymphocytes (CTL) recognizing conserved fragments of a pathogen's proteome could greatly impact infectious diseases and cancers. Enabling this potential are recent advances in mass spectrometry that identify specific target peptides among the myriad HLA-bound peptides on altered cells. Ultrasensitivity of these physical detection methods allows for the direct assessment of peptide presentation on small numbers of tissue-derived cells. In addition, concurrent advances in immunobiology suggest ways to induce CTLs with requisite functional avidity and tissue deployment. Elicitation of high-avidity resident-memory T cells through vaccination may shift the vaccinology paradigm both for preventive and therapeutic approaches to human disease control.
3-D integration of MQW SEED detectors and modulators over active sub-micron CMOS circuits: Application to a 2KBit parallel photonic page buffer (2002)

The efficacy of many system-designs based on free-space optical interconnects and smart-pixels, depends on the availability of a flexible, high-density, silicon-compatible, optoelectronic technology platform. To this end, we demonstrate the hybrid 3D integration of GaAs-AlGaAs 850nm multiple quantum well (MQW) detectors and modulators directly over active 0.8 /spl mu/m silicon CMOS circuits. To test this technique, a self electro-optic effect device (SEED) input-light detector was flip-chip bonded over a transimpedance receiver circuit, whose output was fed to a simple transmitter circuit and then to another SEED device that served as an output-light modulator.
Answering Binary Causal Questions Through Large-Scale Text Mining: An Evaluation Using Cause-Effect Pairs from Human Experts (2019)

In this paper, we study the problem of answering questions of type "Could X cause Y?" where X and Y are general phrases without any constraints. Answering such questions will assist with various decision analysis tasks such as verifying and extending presumed causal associations used for decision making. Our goal is to analyze the ability of an AI agent built using state-of-the-art unsupervised methods in answering causal questions derived from collections of cause-effect pairs from human experts. We focus only on unsupervised and weakly supervised methods due to the difficulty of creating a large enough training set with a reasonable quality and coverage. The methods we examine rely on a large corpus of text derived from news articles, and include methods ranging from large-scale application of classic NLP techniques and statistical analysis to the use of neural network based phrase embeddings and state-of-the-art neural language models.