gebhart/patrepeval huggingface dataset:
Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials (2020)

Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting.
Predictive Factors And Long-Term Visual Outcomes After Anti-Vascular Endothelial Growth Factor Treatment Of Retinal Angiomatous Proliferation (2019)

Maiko Maruyama-Inoue, Shimpei Sato, Shin Yamane, Kazuaki Kadonosono Department of Ophthalmology, Yokohama City University Medical Center, Yokohama, JapanCorrespondence: Maiko Maruyama-InoueDepartment of Ophthalmology, Yokohama City University Medical Center, 4-57 Urafune-cho, Minami-ku, Yokohama, Kanagawa 232-0024, JapanTel +81 45 261 5656Fax +81 45 253 8490Email maicoo@urahp.yokohama-cu.ac.jpPurpose: To report the results of 9-year follow-up examinations and predictive factors for visual acuity outcome after intravitreal injection of anti-vascular endothelial growth factor (VEGF) agents to treat retinal angiomatous proliferation (RAP).Methods: We conducted a retrospective observational study of 85 treatment-na&amp;amp;iuml;ve eyes in 61 patients (21 men, 40 women; age range, 70&amp;amp;ndash;95 years; mean age, 84.0 years) treated with intravitreal injections of anti-VEGF agents. All patients received three consecutive monthly injections as an induction treatment. During the maintenance phase, the patients received intravitreal injections as needed or fixed dosing. The primary outcome measures were best-corrected visual acuity (BCVA) during the follow-up period. Furthermore, we investigated potential predictive factors of improvement in visual acuity. The proportion of patients who developed specific complications were also analyzed.Results: The mean BCVA gradually decreased from 0.58 at baseline to 0.70 at 36 months (P = 0.146), 0.82 at 48 months (P = 0.004), and 0.92 at 108 months (P = 0.021). Improvement in visual acuity at the final visits was associated with baseline visual acuity and central foveal thickness. Massive subretinal hemorrhage, fibrotic scars, and macular atrophy developed in 4 (4.7%), 9 (10.6%), and 50 (56.8%) eyes, respectively, at the final visits, and were all significantly associated with final visual acuity (P = 0.013, P &amp;amp;lt; 0.001, and P = 0.001, respectively).Conclusion: Long-term stabilization of vision in patients with RAP, regardless of treatment modality, was difficult to achieve by using intravitreal injections of anti-VEGF agents. Earlier detection and treatment are important to maintain visual acuity in patients with RAP.Keywords: ranibizumab, aflibercept, retinal angiomatous proliferation, age-related macular degeneration, intravitreal injection\n&amp;amp;nbsp;
Erratum: “Improved hydrogen detection sensitivity in N-polar GaN Schottky diodes” [Appl. Phys. Lett. 94, 212108 (2009)] (2009)

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Plasma Volume Changes Induced by Hypertonic Hemodiafiltration and Standard Hemodialysis (1987)

We have previously reported that treatment of uremia by hypertonic hemodiafiltration (H-HDF) results in a more stable hemodynamic response as compared to standard hemodialysis (HD). The purpose of this study was to determine if plasma volume (PV) preservation was a significant factor in this response. Nine patients were studied during single treatment sessions of H-HDF and HD. Both sessions were 3 h in duration and the ultrafiltration rate and volume were matched. 10 microCi of 125I human serum albumin were injected 40 min before each session for measurement of PV. Changes in PV during the session were determined from the change in plasma albumin concentration and the hematocrit. The decrease in PV was significantly less during H-HDF. This was associated with a significantly higher plasma sodium and osmolality. The calculated effective osmolality during H-HDF was not only higher than in HD, but showed a significant increase at 2 and 3 h when compared to the baseline level (p less than 0.05). The calculated volume of extravascular mobilization was higher during H-HDF and is probably the mechanism of the PV preservation. In conclusion, this study demonstrates that PV is preserved during H-HDF better than during HD as a result of a more adequate plasma refilling; this appears to be mediated by an increased plasma effective osmolality.
The effects of pulsed electromagnetic fields on membrane transport, protein and ATP synthesis in rat skin (1984)

Conference Article| June 01 1984 The effects of pulsed electromagnetic fields on membrane transport, protein and ATP synthesis in rat skin PIET H. DELPORT; PIET H. DELPORT *Afdelingen Biochemie, Orthopedie, Electrotechniek, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium Search for other works by this author on: This Site PubMed Google Scholar NGOK CHENG; NGOK CHENG *Afdelingen Biochemie, Orthopedie, Electrotechniek, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium Search for other works by this author on: This Site PubMed Google Scholar JOSEPH C. MULIER; JOSEPH C. MULIER †Orthopedie, Electrotechniek, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium Search for other works by this author on: This Site PubMed Google Scholar WILLY M. SANSEN; WILLY M. SANSEN ‡Electrotechniek, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium Search for other works by this author on: This Site PubMed Google Scholar WILLIAM DE LOECKER WILLIAM DE LOECKER *Afdelingen Biochemie, Orthopedie, Electrotechniek, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1984) 12 (3): 437–438. https://doi.org/10.1042/bst0120437 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation PIET H. DELPORT, NGOK CHENG, JOSEPH C. MULIER, WILLY M. SANSEN, WILLIAM DE LOECKER; The effects of pulsed electromagnetic fields on membrane transport, protein and ATP synthesis in rat skin. Biochem Soc Trans 1 June 1984; 12 (3): 437–438. doi: https://doi.org/10.1042/bst0120437 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1984 Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.
CCDC 975015: Experimental Crystal Structure Determination (2013)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
The Microtubule-associated Histone Deacetylase 6 (HDAC6) Regulates Epidermal Growth Factor Receptor (EGFR) Endocytic Trafficking and Degradation (2010)

Histone deacetylase 6 (HDAC6) is a microtubule-associated deacetylase with tubulin deacetylase activity, and it binds dynein motors. Recent studies revealed that microtubule acetylation affects the affinity and processivity of microtubule motors. These unique properties implicate a role for HDAC6 in intracellular organelle transport. Here, we show that HDAC6 associates with the endosomal compartments and controls epidermal growth factor receptor (EGFR) trafficking and degradation. We found that loss of HDAC6 promoted EGFR degradation. Mechanistically, HDAC6 deficiency did not cause aberrant EGFR internalization and recycling. Rather, it resulted in accelerated segregation of EGFR from early endosomes and premature delivery of EGFR to the late endosomal and lysosomal compartments. The deregulated EGFR endocytic trafficking was accompanied by an increase in microtubule-dependent movement of EGFR-bearing vesicles, revealing a novel regulation of EGFR vesicular trafficking and degradation by the microtubule deacetylase HDAC6.
Learning Deep Contextual Attention Network for Narrative Photo Stream Captioning (2017)

While image captioning has been extensively studied, the problem of generating narrative descriptions for photo streams still remains under explored. Photo stream captioning is more challenging due to the large visual variance, complicated object context, and sentence-to-sentence coherence in the ordered collection of photos. To deal with these challenges, we propose a novel deep contextual attention network (CAN) to narratively describe photo streams by jointly exploring the rich context among attended regions and the coherence in sentences. The proposed CAN is designed in an encoder-decoder framework: the encoder models visual contexts via region-level bilinear similarity and selectively focuses on the attention areas with salient context; while a novel hierarchical gated recurrent unit (h-GRU) acts as the decoder to effectively preserve the semantic coherence among the generated sentences. As CAN is capable to exploit visual attention and context in the photo stream, the generated story is more semantically coherent than merely concatenating the isolated individual image captions. We conduct experiments on the SIND dataset and show that CAN outperforms the state-of-the-art methods by 3.1%, 8.9%, and 9.1% in terms of BLEU, METEOR and CIDEr, respectively.
An Interaction-based Video Viewing Support System using Geographical Relationships (2020)

With the spread of internet television, many studies have been conducted to recommend relevant information for TV programs. Such as NHK Hybridcast is a new TV service that provides relevant information on the same screen during a TV program broadcast. However, current services cannot recommend supplementary information for TV programs based on user viewing behavior. Therefore, in this paper, we propose a video viewing support system to recommend supplementary information using geographical relationships based on user interaction.
XSLT Cookbook (2002)

From the Publisher:
The XSLT Cookbook is a collection of hundreds of solutions to problems that XSLT developers regularly face. The recipes range from simple string manipulation and mathematical processing to more complex topics such as extending XSLT, testing and debugging XSLT stylesheets, and graphics creation with SVG. Recipes can be run directly or tweaked to fit your particular application's needs more precisely. Each recipe walks through a problem and a solution, with explanations of the choices made and techniques used in creating that solution. Many recipes include alternative solutions and explore issues like convenience and performance. The XSLT Cookbook is an ideal companion both for developers who are still figuring out XSLT's template-based approach and who want to learn by example and for developers who know XSLT and want a collection of quickly reusable recipes. XSLT frequently offers a number of ways to perform a transformation, and the best solution may not always be the most straightforward. The recipes in this Cookbook demonstrate and explain XSLT's template-based logic, a frequent stumbling block for developers new to XSLT.
Supplementary Figure 7 from Unique and Novel Urinary Metabolomic Features in Malignant versus Benign Adrenal Neoplasms (2023)

&lt;p&gt;Comparison between patients with ACC and benign adrenal disease with respect to creatine riboside, Feature 1, Feature 6, and NE-trimethlylysine that were detected in the tissue: (A) creatine riboside, (B) m/z 306.153, (C) m/z 334.186, and (D) NE-trimethyllysine.&lt;/p&gt;
Biofilm formation of ica operon‐positive Staphylococcus epidermidis from different sources (2015)

Information on the prevalence of biofilm-related factors (PIA, Bhp, Aap, Embp) in Staphylococcus epidermidis of animal origin is scarce. In this study, 263 S. epidermidis isolates of diverse origin (animal, farmers, patients, and laboratory staff) were investigated for the presence of the ica operon (icaRADBC). The icaRADBC-positive isolates were further characterized by means of biofilm formation, presence of other biofilm-related genes, antimicrobial resistance, and population structure. Of all isolates, 28.5% (n = 75) were icaRADBC-positive, including 16.5% of animal origin, 29.1% farmer isolates, and 44.6% hospital-associated isolates (including patients and laboratory staff isolates). Most icaRADBC-positive isolates carried embp (n = 73), aap (n = 57), bhp (n = 22), and IS256 (n = 29). Statistical differences were found between animal and patient isolates for the presence of icaRADBC, bhp, and aap. No statistically significant relation was found between the presence of one or more genes and the level of biofilm formation. Most icaRADBC-positive isolates belonged to the clonal complex 5 (formerly 2) and most sequence types corresponded to types previously observed in community and nosocomial S. epidermidis populations. Although the prevalence of S. epidermidis in the nasal cavity of bovines and poultry is low, some isolates belong to STs related to ica-positive clinical strains.
Improving the barrier function of damaged cultured urothelium using chondroitin sulfate (2019)

CS instillation improves the recovery of the urothelial barrier after damage in vitro. This functional experiment shows that CS improves recovery of damaged urothelial function, which supports the hypothesis behind the mechanism of action of GAG-replenishment therapy.
ChemInform Abstract: A Fast and Inexpensive Method for N‐Terminal Fluorescein‐Labeling of Peptides. (1998)

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.
Development of resistance to metronidazole and minocycline in vitro (1997)

By local delivery of antibiotics to periodontal pockets, very high initial concentrations are often quickly succeeded by subinhibitory concentrations, which may facilitate development of bacterial resistance. The purpose of the present study was to investigate possible development of resistance in suspected periodontal pathogens after exposure to subinhibitory concentrations of metronidazole and minocycline. The minimal inhibitory concentration (MIC) of 18 reference strains and 12 clinical isolates was determined by a broth dilution method. Subsequently, all strains with MIC < 8 micrograms/ml were exposed to serial passage on plates containing subinhibitory and gradually increasing concentrations of antibiotics, until growth was inhibited. Initially, most strains were inhibited at < or = 0.250 microgram/ml of minocycline and < or = 0.5 microgram/ml of metronidazole, though A. actinomycetemcomitans was resistant to metronidazole. After growth at subinhibitory concentrations, 8 strains survived 1-2 x and 11 stains survived 8-32 x their initial MIC of metronidazole, growing at up to 8 micrograms/ml. All A. actinomycetemcomitans survived 8-64 x their initial MIC of minocycline, growing at > or = 2 micrograms/ml, while all other strains were inhibited at < or = 0.250 microgram/ml, corresponding to a 1-8 x increase in their initial MIC. Thus, development of resistance was observed for periodontal bacteria growing at up to 64 x their initial MIC, but the final level of resistance was moderate.
<title>Epitaxial YBa<formula><inf><roman>2</roman></inf></formula>Cu<formula><inf><roman>3</roman></inf></formula>O<formula><inf><roman>7</roman></inf></formula> superconducting infrared microbolometers on silicon</title> (1994)

Superconducting transition-edge infrared microbolometers have been fabricated by silicon micromachining using an epitaxial YLa<SUB>.05</SUB>Ba<SUB>1.95</SUB>Cu<SUB>3</SUB>O<SUB>7-x</SUB> (YBCO) film on a epitaxial yttria-stabilized zirconia buffer layer on silicon. The low thermal conductance of the micromachined structures combined with the sharp resistance change at the superconducting transition results in very sensitive infrared detectors. The broadband response of these thermal detectors makes them particularly useful at wavelengths longer than the typical operating range of semiconductor detectors ((lambda) greater than about 20 micrometers ) at moderately high temperatures (T approximately 70 K and higher). The use of standard silicon processing promises low-cost monolithic integration of the readout electronics for arrays of these devices. Preliminary measurements are reported here on a device 140 micrometers X 105 micrometers in size with a detectivity, D*, of 8 +/- 2 X 10<SUP>9</SUP> cm Hz<SUP>1/2</SUP>/Watt, and NEP of 1.5 X 10<SUP>-12</SUP> Watts/Hz<SUP>1/2</SUP> at 2 Hz and 80.7 K. This value of D* exceeds the highest previously reported D* for a YBCO transition-edge bolometer, and is comparable to the highest reported D* for a thermal detector operating at greater than about 70 K. The thermal time constant for this device was 105 +/- 20 msec.
BIOMIMETIC LIGHT WEIGHT COMPOSITE STRUCTURE WITH HONEYCOMB-TRABECULA (2005)

In order to develop light-weight biomimetic composites, the microstructure of A.dichotoma was investigated in detail. A three dimensional honeycomb-columniation model was proposed and several design concepts for further development of three dimensional composite structure were discussed. At the same time, the advantages and application possibility were described. The results show that there is an integrity network-columniation structure in the whole fore wings of A.dichotoma. This network structure is made of air sacs, and although it presents the (irregularity) and diversification, it is almost similar to the honeycomb-shaped polygon structure.
COMMENTARY ON THE PLEASURES OF SOLVING IMPOSSIBLE PROBLEMS OF EXPERIMENTAL PHYSIOLOGY (2005)

This commentary presents a series of examples of "impossible experimental problems" that we have encountered over the years in addressing various challenging questions in physiology. We aim to show how stimulating the challenges of physiology can be and demonstrate how our naive invocation of methods from disparate fields of science and engineering has led to delightful resolutions of physiological challenges that were utterly new to this intrepid interdisciplinary researcher.
Noninvasive MR imaging of magnetically labeled stem cells to directly identify neovasculature in a glioma model (2004)

Bone marrow-derived endothelial precursor cells incorporate into neovasculature and have been successfully used as vehicles for gene delivery to brain tumors. To determine whether systemically administered Sca1+ bone marrow cells labeled with superparamagnetic iron oxide nanoparticles can be detected by in vivo magnetic resonance imaging in a mouse brain tumor model, mouse Sca1+ cells were labeled in vitro with ferumoxides-poly-L-lysine complexes. Labeled or control cells were administered intravenously to glioma-bearing severe combined immunodeficient (SCID) mice. Magnetic resonance imaging (MRI) was performed during tumor growth. Mice that received labeled cells demonstrated hypointense regions within the tumor that evolved over time and developed a continuous dark hypointense ring at a consistent time point. This effect was not cleared by administration of a gadolinium contrast agent. Histology showed iron-labeled cells around the tumor rim in labeled mice, which expressed CD31 and von Willebrand factor, indicating the transplanted cells detected in the tumor have differentiated into endothelial-like cells. These results demonstrate that MRI can detect the incorporation of magnetically labeled bone marrow-derived precursor cells into tumor vasculature as part of ongoing angiogenesis and neovascularization. This technique can be used to directly identify neovasculature in vivo and to facilitate gene therapy by noninvasively monitoring these cells as gene delivery vectors.
LDCA: Lightweight Dynamic Clustering Algorithm for IoT-Connected Wide-Area WSN and Mobile Data Sink Using LoRa (2021)

Wide-area monitoring applications of the Internet-of-Things (IoT) connected wireless sensor network (WSN) consists of sensor nodes (SNs) with limited hardware and energy sources. The distributed nature of such a network and the difficulty of remote access make it more demanding to design an energy-efficient WSN. Moreover, long-range and low-power wireless connectivity is a challenge in IoT-connected applications. Present WSN topologies deal mainly with fixed SNs, SN distribution, and fixed data sink (DS). The majority of the control layer is implemented in the lower hierarchical layer or in a virtual middle layer, which reduces the network lifetime due to excessive processing and data transmission activities. This article proposes a real-time lightweight dynamic clustering algorithm (LDCA) for a WSN that supports the following two scenarios with limited processing resources: 1) with mobile DSs and static SNs (such as DS and SNs mounted on unmanned aerial vehicles, autonomous vehicles) and 2) with mobile SNs and static DSs (such as livestock monitoring or autonomous robots in smart farming, and urban monitoring). The proposed algorithm is based on the received signal strength indicator and signal-to-noise ratio of a long-range (LoRa) interface and its residual energy. Mathematical models were derived for real-time clustering using LoRa. Memory requirement and clustering efficiency of the constrained SN and DS for various mobility scenario were evaluated. The proposed LDCA reduces the energy requirement to 33% compared to static clustering, by reducing the number of concurrent clusters and hops. In addition, a hardware-based approach was used to validate the LDCA algorithm, and evaluate its performance in terms of energy efficiency, packet delivery rate, and network lifetime.