gebhart/patrepeval huggingface dataset:
Distinct Patterns of Cleavage and Translocation of Cell Cycle Control Proteins in CD95-induced and p53-induced apoptosis (2003)

Apoptotic cell death induced by p53 occurs at a late G1 cell cycle checkpoint termed the restriction (R) point, and it has been proposed that p53-induced apoptosis causes upregulation of CD95. However, as cells with defective in CD95 signaling pathway are still sensitive to p53-induced apoptosis, CD95 cannot be the sole factor resulting in apoptosis. In addition, unlike p53-induced apoptosis, the relationship between CD95-mediated apoptosis and the cell cycle is not clearly understood. It would therefore be worth investigating whether CD95-mediated cell death is pertinent with p53-induced apoptosis in view of cell cycle related molecules. In this report, biochemical analysis showed that etoposide-induced apoptosis caused the induction and the nuclear translocation of effector molecules involved in G1 cell cycle checkpoint. However, there was no such translocation in the case of CD95-mediated death. Thus, although both types of apoptosis involved caspase activation, the cell cycle related proteins responded differently. This argues against the idea that p53-induced apoptosis occurs through the induction of CD95/CD95L expression.
Mapping Pulsatile Optic Nerve Head Deformation Using OCT (2022)

The computational pipeline demonstrated good reproducibility and had the capacity to accurately map the pulsatile deformation of the optic nerve. In a clinical setting, we detected physiological changes in normal subjects supporting its translation potential as a novel biomarker for the diagnosis and progression of optic nerve diseases.
Study of photosensitizer for i-line lithography (1992)

In this paper, diazo derivatives having various ballasts are newly evaluated as the sensitizers for i-line resist system. The selection of the ballast of the sensitizer can be executed on the basis of Dill's A parameter. The derivation of a mathematical expression, which is usable for the optimization of the quantity of a sensitizer in resist system, is also described. The experimentally obtained optimal value is confirmed to show a good fit with the value given by the expression.
A basic study of MATRIX motor (2011)

This paper describes the characteristics of a new concept motor which can excite arbitrary waveforms. The motor is based on PMSM and the armature windings of the motor are consist of multi-layer concentrated windings connected by many semiconductor switches. The motor is named “Matrix motor” because the switches are turned on or off by the command of matrix. Various winding connection makes the arbitrary excitation waveforms, for example, the concentrated winding excitation, the distributed winding excitation, the multi harmonic excitation, and so on. The motor can realize a variable characteristic by changing its excitation. This paper shows the principle of the motor and its effectiveness is verified by the experimental results and the simulation results.
Kinetic profiling of therapeutic strategies for inhibiting the formation of amyloid oligomers (2022)

Protein self-assembly into amyloid fibrils underlies several neurodegenerative conditions, including Alzheimer's and Parkinson's diseases. It has become apparent that the small oligomers formed during this process constitute neurotoxic molecular species associated with amyloid aggregation. Targeting the formation of oligomers represents, therefore, a possible therapeutic avenue to combat these diseases. However, it remains challenging to establish which microscopic steps should be targeted to suppress most effectively the generation of oligomeric aggregates. Recently, we have developed a kinetic model of oligomer dynamics during amyloid aggregation. Here, we use this approach to derive explicit scaling relationships that reveal how key features of the time evolution of oligomers, including oligomer peak concentration and lifetime, are controlled by the different rate parameters. We discuss the therapeutic implications of our framework by predicting changes in oligomer concentrations when the rates of the individual microscopic events are varied. Our results identify the kinetic parameters that control most effectively the generation of oligomers, thus opening a new path for the systematic rational design of therapeutic strategies against amyloid-related diseases.
Specific Inhibitor of Placental Alkaline Phosphatase Isolated from a DNA-Encoded Chemical Library Targets Tumor of the Female Reproductive Tract (2021)

Placental alkaline phosphatase (PLAP) is an abundant surface antigen in the malignancies of the female reproductive tract. Nevertheless, the discovery of PLAP-specific small organic ligands for targeting applications has been hindered by ligand cross-reactivity with the ubiquitous tissue non-specific alkaline phosphatase (TNAP). In this study, we used DNA-encoded chemical libraries to discover a potent (IC<sub>50</sub> = 32 nM) and selective PLAP inhibitor, with no detectable inhibition of TNAP activity. Subsequently, the PLAP ligand was conjugated to fluorescein; it specifically bound to PLAP-positive tumors <i>in vitro</i> and targeted cervical cancer <i>in vivo</i> in a mouse model of the disease. Ultimately, the fluorescent derivative of the PLAP inhibitor functioned as a bispecific engager redirecting the killing of chimeric antigen receptor-T cells specific to fluorescein on PLAP-positive tumor cells.
Resection of Isolated Fossa Recurrence of Renal-Cell Carcinoma After Nephrectomy Using Hand-Assisted Laparoscopy (2002)

A 72-year-old woman with a body mass index of 33.6 had an apparently isolated renal fossa recurrence of a Grade II, Stage T(3) renal-cell carcinoma. The lesion was resected using hand-assisted laparoscopy with rapid recovery and good short-term results.
Double‐row 18‐loop transceive–32‐loop receive tight‐fit array provides for whole‐brain coverage, high transmit performance, and SNR improvement near the brain center at 9.4T (2018)

In general, the new approach of constructing a single-layer array consisting of both TxRx- and Rx-only elements simplifies the array construction by minimizing the total number of elements and makes the entire design more robust and, therefore, safe. Overall, our work provides a recipe for a Tx- and Rx-efficient head array coil suitable for parallel transmission and reception as well as whole-brain imaging at UHF.
Expansion of Human Hematopoietic Stem/Progenitor Cells on Decellularized Matrix Scaffolds (2014)

Umbilical cord blood (UCB) is one of the richest sources for hematopoietic stem/progenitor cells (HSPCs), with more than 3000 transplantations performed each year for the treatment of leukemia and other bone marrow, immunological, and hereditary diseases. However, transplantation of single cord blood units is mostly restricted to children, due to the limited number of HSPC per unit. This unit develops a method to increase the number of HSPCs in laboratory conditions by using cell-free matrices from bone marrow cells that mimic 'human-body niche-like' conditions as biological scaffolds to support the ex vivo expansion of HSPCs. In this unit, we describe protocols for the isolation and characterization of HSPCs from UCB and their serum-free expansion on decellularized matrices. This method may also help to provide understanding of the biochemical organization of hematopoietic niches and lead to suggestions regarding the design of tissue engineering-based biomimetic scaffolds for HSPC expansion for clinical applications.
Three‐Dimensional Printing and Its Applications in Otorhinolaryngology–Head and Neck Surgery (2016)

Objective Three-dimensional (3D)-printing technology is being employed in a variety of medical and surgical specialties to improve patient care and advance resident physician training. As the costs of implementing 3D printing have declined, the use of this technology has expanded, especially within surgical specialties. This article explores the types of 3D printing available, highlights the benefits and drawbacks of each methodology, provides examples of how 3D printing has been applied within the field of otolaryngology-head and neck surgery, discusses future innovations, and explores the financial impact of these advances. Data Sources Articles were identified from PubMed and Ovid MEDLINE. Review Methods PubMed and Ovid Medline were queried for English articles published between 2011 and 2016, including a few articles prior to this time as relevant examples. Search terms included 3-dimensional printing, 3 D printing, otolaryngology, additive manufacturing, craniofacial, reconstruction, temporal bone, airway, sinus, cost, and anatomic models. Conclusions Three-dimensional printing has been used in recent years in otolaryngology for preoperative planning, education, prostheses, grafting, and reconstruction. Emerging technologies include the printing of tissue scaffolds for the auricle and nose, more realistic training models, and personalized implantable medical devices. Implications for Practice After the up-front costs of 3D printing are accounted for, its utilization in surgical models, patient-specific implants, and custom instruments can reduce operating room time and thus decrease costs. Educational and training models provide an opportunity to better visualize anomalies, practice surgical technique, predict problems that might arise, and improve quality by reducing mistakes.
Catecholate Siderophores Protect Bacteria from Pyochelin Toxicity (2012)

We have shown that the catecholate siderophore enterobactin protects E. coli against the toxic effects of pyochelin by reducing ROS. Thus, it appears that catecholate siderophores can behave as protectors of oxidative stress. These results support the idea that siderophores can have physiological roles aside from those in iron acquisition.
Supplementary Figures S1-S5 from Active Ras Triggers Death in Glioblastoma Cells through Hyperstimulation of Macropinocytosis (2023)

Supplementary Figures S1-S5 from Active Ras Triggers Death in Glioblastoma Cells through Hyperstimulation of Macropinocytosis
MOLECULAR STARK EFFECT MEASUREMENTS IN BROADBAND CHIRPED-PULSE FOURIER TRANSFORM MICROWAVE (CP-FTMW) SPECTROMETERS (2008)

Preoperative identification of the arachnoid cyst wall and surrounding anatomical structures by MRC may help avoid complications and allow safer neuroendoscopic surgery.
Modeling and generalization of parallel multilevel converter for the design of the closed loop's controllers (2017)

Connecting legs in parallel in a buck convertor is a way to increase the output current by improving the output's waveforms. By coupling these legs, it is possible to reduce the current ripple and thus the coil volume; however this coupling adds internal variables which must be controlled in order to prevent saturation of the iron core in the couplers and keep the linearity of the system. This paper deals with the modeling of parallel multilevel converters according to the number of legs and their coupling using different methods for the purpose of achieving a balancing controller. A study on the generalization of the sizing of the controllers is also presented and experimental results are shown to verify the validity of the model.
The role of the manager in a noncooperative network (2002)

Traditional computer networks were typically designed with system-wide optimization in mind. In noncooperative networks users make control decisions that optimize their individual performance objectives. Nash equilibria characterize the operating points of such networks. Nash equilibria exhibit, in general, suboptimal network performance. Focusing on routing, a methodology is devised for overcoming this deficiency, through the intervention of the network manager. The manager controls part of the network flow, is aware of the noncooperative behavior of the users and performs its routing aiming at improving the overall system performance. The existence of maximally efficient strategies for the manager, i.e., strategies that drive the system into the global network optimum, is investigated. Necessary and sufficient conditions for the existence of a maximally efficient strategy are derived. The maximally efficient strategy are shown to be unique and it is specified explicitly.
Epidermal growth factor (EGF/URO) induces expression of regulatory peptides in damaged human gastrointestinal tissues (1990)

The pS2 gene encodes for a small cysteine-rich protein, and was originally found by differential screening of a cDNA library from the human breast carcinoma cell line, MCF-7. The presence of pS2 is closely correlated with oestrogen dependence in breast carcinomas. While the function of pS2 is unknown, pS2 protein has been shown to be homologous with the gastrointestinal peptide hormone pancreatic spasmolytic polypeptide (PSP) and its human counterpart hSP, in which a 5-cysteine domain is tandemly repeated. The 5' flanking region of the pS2 gene contains an enhancer region responsive to oestrogens and to epidermal growth factor (EGF/URO). We now report that pS2 and hSP expression occurs in a wide range of endodermally-derived tissues, including the duodenum, the pancreas, and in a recently defined cell lineage associated with chronic gastrointestinal ulceration. In each case, this expression was associated with secretion of immunoreactive EGF/URO. We further show that the co-expression of pS2 and hSP in gastric surface epithelial cells is also associated with the secretion of EGF/URO in the subjacent mucous neck cells. Our results indicate that local EGF/URO secretion induces pS2 and hSP in adjacent cells, and that these molecules are then available to participate in pathophysiological responses. The finding of similar patterns of EGF/URO, hSP and pS2 expression in association with chronic damage suggests that this is a fundamental response in the healing of these tissues.
Structure, heat capacity and Raman spectra of Ba2MgWO6 single crystals grown in BaCl2-MgCl2 flux (2023)

We present a new method of Ba2MgWO6 single crystal synthesis that allows to grow larger crystals using a BaCl2 and MgCl2 flux. Difficulties to grow single crystals of a size suitable for macroscopic material property measurements caused the majority of characterisation being published on polycrystalline samples. Our single crystal diffraction and energy dispersive X-ray analysis confirmed high quality of synthesised samples. Heat capacity measurements from 300 K to 2 K do not show any phase transitions. However, Raman spectra measured down to 77 K contain additional weak peaks at all temperatures probed, which is in a contrast with only 4 Raman active modes expected from the crystal structure with the space group Fm3¯m. This calls for a more detailed study of potential symmetry breaking that could also influence the electronic properties of the material.
Integrated Quantum Frequency Comb Source of Entangled Qubits (2016)

We demonstrate the simultaneous generation of multiple time-bin entangled photon pairs on a CMOS-compatible photonic chip. We measure quantum interference and perform state tomography, confirming entangled qubits with fidelities above 86% and 99.9% purity.
Lateral Root Initiation and the Analysis of Gene Function Using Genome Editing with CRISPR in Arabidopsis (2021)

Lateral root initiation is a post-embryonic process that requires the specification of a subset of pericycle cells adjacent to the xylem pole in the primary root into lateral root founder cells. The first visible event of lateral root initiation in <i>Arabidopsis</i> is the simultaneous migration of nuclei in neighbouring founder cells. Coinciding cell cycle activation is essential for founder cells in the pericycle to undergo formative divisions, resulting in the development of a lateral root primordium (LRP). The plant signalling molecule, auxin, is a major regulator of lateral root development; the understanding of the molecular mechanisms controlling lateral root initiation has progressed tremendously by the use of the <i>Arabidopsis</i> model and a continual improvement of molecular methodologies. Here, we provide an overview of the visible events, cell cycle regulators, and auxin signalling cascades related to the initiation of a new LRP. Furthermore, we highlight the potential of genome editing technology to analyse gene function in lateral root initiation, which provides an excellent model to answer fundamental developmental questions such as coordinated cell division, growth axis establishment as well as the specification of cell fate and cell polarity.
TU-B-220-04: 3D Inverse Scattering and Refraction Corrected Reflection Ultrasound (2011)

Purpose: Establish the ability of our 3D breast scanner to present 360 degree compounded reflection images coincident and registered with speed and attenuation maps generated by the same machine. Methods: We generate a 3D map of speed and attenuation using our unique algorithms and data acquisition hardware. From these we use the eikonal equation and ray tracing to correct for refraction and attenuation loss. The back-propagated reflected energy is thus placed in the correct position in a fixed coordinate system, independent of view, allowing 360 degree compounding. To recover ‘posterior beam’ artifacts that are part of the BI-RADS criteria we generate ‘clock views’ at each hour position by compounding over 3 views. The reflection data acquisition hardware consists of 3 linear arrays of 192 elements, each 0.375 mm in width. The arrays are focused for short, medium and long ranges with overlapping fields of view to yield a conglomerate large field of view. They are 4, 7.5, and 14 mm tall, respectively, with geometric foci of 20, 45, and 70 mm, respectively. The array centers are 105 mm from the scanner axis of rotation and are tilted upward 10 degrees from the horizontal to aid in data acquisition near the chest wall. By utilizing data from each array in its appropriate field of view we preserve vertical resolution. The arrays are 46 degrees apart and views are collected at 60 positions, 6 degrees apart, for all arrays. Results: We present correlated panels of our speed and reflection images that compounded over a 360 degree aperture for patient cases with both benign and malignant biopsy results in comparison to sonography. Conclusions: Our unique DICOM compliant 3D volumes of speed, attenuation and reflection provide high resolution information precisely coincident and registered not available with any other form of ultrasound imaging. TechniScan, Inc., Salt Lake City, Utah
The effect of geriatric intervention in frail older patients receiving chemotherapy for colorectal cancer: a randomised trial (GERICO) (2021)

Abstract Background Older patients with colorectal cancer (CRC) experience chemotherapy dose reductions or discontinuation. Comprehensive geriatric assessment (CGA) predicts survival and chemotherapy completion in patients with cancer, but the benefit of geriatric interventions remains unexplored. Methods The GERICO study is a randomised Phase 3 trial including patients ≥70 years receiving adjuvant or first-line palliative chemotherapy for CRC. Vulnerable patients (G8 questionnaire ≤14 points) were randomised 1:1 to CGA-based interventions or standard care, along with guideline-based chemotherapy. The primary outcome was chemotherapy completion without dose reductions or delays. Secondary outcomes were toxicity, survival and quality of life (QoL). Results Of 142 patients, 58% received adjuvant and 42% received first-line palliative chemotherapy. Interventions included medication changes (62%), nutritional therapy (51%) and physiotherapy (39%). More interventional patients completed scheduled chemotherapy compared with controls (45% vs. 28%, P = 0.0366). Severe toxicity occurred in 39% of controls and 28% of interventional patients ( P = 0.156). QoL improved in interventional patients compared with controls with the decreased burden of illness ( P = 0.048) and improved mobility ( P = 0.008). Conclusion Geriatric interventions compared with standard care increased the number of older, vulnerable patients with CRC completing adjuvant chemotherapy, and may improve the burden of illness and mobility. Trial registration ClinicalTrials.gov ID: NCT 02748811.
Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics (2017)

Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.
Improved Detection of Recurrent Hepatocellular Carcinomas in Arterial Phase With CAIPIRINHA-Dixon-TWIST-Volumetric Interpolated Breath-Hold Examination (2016)

Compared with the equivalent-to-conventional single arterial phase, MA-CDT-VIBE with 6 arterial subphases demonstrated higher detection rate of recurrent HCCs in arterial phase and provided a wider arterial observation window, especially for recurrent HCCs less than 2 cm in diameter.
Experiences in Lightweight Event Relaying Framework Design (2010)

In software development there is always the need for faster development process. One way to speed up the process is to reuse existing components, in which loose coupling of the components is an important prerequisite. Publish/subscribe is one popular way to provide loose coupling, and there exists many middleware solutions for it. However, most such solutions are aimed for large inter-device networks, and are poorly suited for resource-constrained low-level contexts. As our solution we present the design of SERF, a novel lightweight software framework implementing pub/sub event messaging and peer-to-peer architectures. We also describe the experiences and lessons learned that led to the development of the framework. Upon analysis we find out that SERF offers the advantages of loosely coupled modules and pub/sub, but also point out that the framework is less suitable outside its framed problem area.