gebhart/patrepeval huggingface dataset:
Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types (2022)

Soft tissue sarcomas are pleiotropic tumors of mesenchymal cell origin. These tumors are rare in humans but common in veterinary practice, where they comprise up to 15% of canine skin and subcutaneous cancers. Because they present similar morphologies, primary sites, and growth characteristics, they are treated similarly, generally by surgical resection followed by radiation therapy. Previous studies have examined a variety of genetic changes as potential drivers of tumorigenesis and progression in soft tissue sarcomas as well as their use as markers for soft tissue sarcoma subtypes. However, few studies employing next generation sequencing approaches have been published. Here, we have examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors. We provide a computational framework for using resulting data to categorize tumors, perform cross species comparisons and identify genetic changes associated with tumorigenesis. Functional overrepresentation analysis of differentially expressed genes further implicate both common and tumor-type specific transcription factors as potential mediators of tumorigenesis and aggression. Implications for tumor-type specific therapies are discussed. Our results illustrate the potential utility of this approach for the discovery of new therapeutic approaches to the management of canine soft tissue sarcomas and support the view that both common and tumor-type specific mechanisms drive the development of these tumors.
Second-line Eribulin in Triple Negative Metastatic Breast Cancer patients. Multicentre Retrospective Study: The TETRIS Trial (2021)

<b>Introduction:</b> Large and consistent evidence supports the use of eribulin mesylate in clinical practice in third or later line treatment of metastatic triple negative breast cancer (mTNBC). Conversely, there is paucity of data on eribulin efficacy in second line treatment. <b>Methods:</b> We investigated outcomes of 44 mTNBC patients treated from 2013 through 2019 with second line eribulin mesylate in a multicentre retrospective study involving 14 Italian oncologic centres. <b>Results:</b> Median age was 51 years, with 11.4% of these patients being metastatic at diagnosis. Median overall survival (OS) and progression free survival (PFS) from eribulin starting were 11.9 (95%CI: 8.4-15.5) and 3.5 months (95%CI: 1.7-5.3), respectively. We observed 8 (18.2%) partial responses and 10 (22.7%) patients had stable disease as best response. A longer PFS on previous first line treatment predicted a better OS (HR=0.87, 95%CI: 0.77-0.99, p= 0.038) and a longer PFS on eribulin treatment (HR=0.92, 95%CI: 0.85-0.98, p=0.018). Progression free survival to eribulin was also favorably influenced by prior adjuvant chemotherapy (HR=0.44, 95%CI: 0.22-0.88, p=0.02). Eribulin was generally well tolerated, with grade 3-4 adverse events being recorded in 15.9% of patients. <b>Conclusions:</b> The outcomes described for our cohort are consistent with those reported in the pivotal Study301 and subsequent observational studies. Further data from adequately-sized, ad hoc trials on eribulin use in second line for mTNBC are warranted to confirm our findings.
REAL-TIME OBSERVATION OF DNA COMFORMATIONAL TRANSITIONS AT A SINGLE-MOLECULE LEVEL BY MICROFLUIDIC DEVICES (2010)

We have developed a precise fluid control and a solution exchange system by a combination of novel microchannel designs and electroosmotic pumps for real-time observation of DNA conformational transitions at a single-molecule level. By using the microfluidic devices, we revealed the stepwise conformational transitions induced by ethanol solution.
Azicemicins A and B, a New Antimicrobial Agent Produced by Amycolatopsis. I. Taxonomy, Fermentation, Isolation, Characterization and Biological Activities. (1995)

A new structural class of the antibiotic, azicemicins A (1) and B (2) were isolated from the culture broth of the strain MJ126-NF4, which was closely related to Amycolatopsis sulphurea. They were purified by adsorption on Diaion HP-20, silica gel column chromatography and preparative TLC. The molecular formulas of 1 and 2 were determined to be C23H25O9N and C22H23O9N by HRFAB-MS, respectively. Azicemicins A and B have moderate growth inhibiting activity against Gram-positive bacteria and mycobacteria.
Metalloenzyme-like catalyzed isomerizations of sugars by Lewis acid zeolites (2012)

Isomerization of sugars is used in a variety of industrially relevant processes and in glycolysis. Here, we show that hydrophobic zeolite beta with framework tin or titanium Lewis acid centers isomerizes sugars, e.g., glucose, via reaction pathways that are analogous to those of metalloenzymes. Specifically, experimental and theoretical investigations reveal that glucose partitions into the zeolite in the pyranose form, ring opens to the acyclic form in the presence of the Lewis acid center, isomerizes into the acyclic form of fructose, and finally ring closes to yield the furanose product. The zeolite catalysts provide processing advantages over metalloenzymes such as an ability to work at higher temperatures and in acidic conditions that allow for the isomerization reaction to be coupled with other important conversions.
Effect of Beam Size on Stone Comminution in Shock Wave Lithotripsy (2009)

The effect of beam size on stone comminution in the Dornier HM‐3 lithotripter were investigated using a modified reflector (MR), which was developed to produce an acoustic field with higher peak pressure and smaller beam size compared to the original reflector (OR) of the HM‐3. The acoustic fields produced at 20 kV by the MR in the focal plane, and by the OR in the focal and pre‐focal plane (z = −15 mm) were characterized using a light spot hydrophone. The efficiencies of stone comminution in a mesh holder were similar, but the corresponding values produced by using the MR in a membrane holder were significantly lower than those produced by the OR in the focal and pre‐focal planes. These results suggest that a broad beam size could increase stone comminution efficiency when fragments are spreading out or moving due to respiratory motion in a large area during SWL. In contrast, when stone fragments are confined and well aligned to lithotripter focus the beam size may not influence significantly the treatment outcome.
Low dose CT-based spatial analysis (CTSA) to measure implant migration after ceramic hip resurfacing arthroplasty (HRA): A phantom study (2023)

Implant migration is a predictor of arthroplasty survivorship. It is crucial to monitor the migration of novel hip prostheses within premarket clinical investigations. RSA is the gold standard method, but requires calibrated radiographs using specialised equipment. A commercial computed tomography micromotion analysis solution is a promising alternative but is not yet available for use with monobloc ceramic implants. This study aimed to develop and validate a CT-based spatial analysis (CTSA) method for use with ceramic implants. A phantom study was undertaken to assess accuracy and precision. A ceramic hip resurfacing arthroplasty (HRA) and 20 tantalum beads were implanted into a synthetic hip model and mounted onto a 6-degree of freedom motion stage. The hip was repeatedly scanned with a low dose CT protocol, with imposed micromovements. Data were interrogated using a semiautomated technique. The effective radiation dose for each scan was estimated to be 0.25 mSv. For the head implant, precision ranged between 0.11 and 0.28 mm for translations and 0.34°-0.42° for rotations. For the cup implant, precision ranged between 0.08 and 0.11 mm and 0.19° and 0.42°. For the head, accuracy ranged between 0.04 and 0.18 mm for translations and 0.28°-0.46° for rotations. For the cup, accuracy ranged between 0.04 and 0.08 mm and 0.17° and 0.43°. This in vitro study demonstrates that low dose CTSA of a ceramic HRA is similar in accuracy to RSA. CT is ubiquitous, and this method may be an alternative to RSA to measure prosthesis migration.
Persistent post–COVID-19 smell loss is associated with immune cell infiltration and altered gene expression in olfactory epithelium (2022)

SARS-CoV-2 causes profound changes in the sense of smell, including total smell loss. Although these alterations are often transient, many patients with COVID-19 exhibit olfactory dysfunction that lasts months to years. Although animal and human autopsy studies have suggested mechanisms driving acute anosmia, it remains unclear how SARS-CoV-2 causes persistent smell loss in a subset of patients. To address this question, we analyzed olfactory epithelial samples collected from 24 biopsies, including from nine patients with objectively quantified long-term smell loss after COVID-19. This biopsy-based approach revealed a diffuse infiltrate of T cells expressing interferon-γ and a shift in myeloid cell population composition, including enrichment of CD207<sup>+</sup> dendritic cells and depletion of anti-inflammatory M2 macrophages. Despite the absence of detectable SARS-CoV-2 RNA or protein, gene expression in the barrier supporting cells of the olfactory epithelium, termed sustentacular cells, appeared to reflect a response to ongoing inflammatory signaling, which was accompanied by a reduction in the number of olfactory sensory neurons relative to olfactory epithelial sustentacular cells. These findings indicate that T cell-mediated inflammation persists in the olfactory epithelium long after SARS-CoV-2 has been eliminated from the tissue, suggesting a mechanism for long-term post-COVID-19 smell loss.
Search for disappearing tracks in proton-proton collisions at s = 8 $$ \sqrt{s}=8 $$ TeV (2015)

A search is presented for long-lived charged particles that decay within the CMS detector and produce the signature of a disappearing track. Disappearing tracks are identified as those with little or no associated calorimeter energy deposits and with missing hits in the outer layers of the tracker. The search uses proton-proton collision data recorded at s = 8 TeV that corresponds to an integrated luminosity of 19.5 fb -1 . The results of the search are interpreted in the context of the anomaly-mediated supersymmetry breaking (AMSB) model. The number of observed events is in agreement with the background expectation, and limits are set on the cross section of direct electroweak chargino production in terms of the chargino mass and mean proper lifetime. At 95% confidence level, AMSB models with a chargino mass less than 260 GeV, corresponding to a mean proper lifetime of 0.2 ns, are excluded.
Prognosis of ramsay hunt syndrome presenting as cranial polyneuropathy (2010)

Ramsay Hunt syndrome associated with cranial polyneuropathy has a good prognosis for FNP and other cranial nerve palsies with a combination therapy of antiviral agents and steroids, but not for recovery of hearing loss.
PhraseFlow: Designs and Empirical Studies of Phrase-Level Input (2021)

Decoding on phrase-level may afford more correction accuracy than on word-level according to previous research. However, how phrase-level input affects the user typing behavior, and how to design the interaction to make it practical remain under explored. We present PhraseFlow, a phrase-level input keyboard that is able to correct previous text based on the subsequently input sequences. Computational studies show that phrase-level input reduces the error rate of autocorrection by over 16%. We found that phrase-level input introduced extra cognitive load to the user that hindered their performance. Through an iterative design-implement-research process, we optimized the design of PhraseFlow that alleviated the cognitive load. An in-lab study shows that users could adopt PhraseFlow quickly, resulting in 19% fewer error without losing speed. In real-life settings, we conducted a six-day deployment study with 42 participants, showing that 78.6% of the users would like to have the phrase-level input feature in future keyboards.
Faculty Opinions recommendation of Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst. (2010)

The enantioselective addition of water to olefins in an aqueous environment is a common transformation in biological systems, but was beyond the ability of synthetic chemists. Here, we present the first examples of a non-enzymatic catalytic enantioselective hydration of enones, for which we used a catalyst that comprises a copper complex, based on an achiral ligand, non-covalently bound to (deoxy)ribonucleic acid, which is the only source of chirality present under the reaction conditions. The chiral β-hydroxy ketone product was obtained in up to 82% enantiomeric excess. Deuterium-labelling studies demonstrated that the reaction is diastereospecific, with only the syn hydration product formed. So far, this diastereospecific and enantioselective reaction had no equivalent in conventional homogeneous catalysis. PMID: 20966958
Ionische Flüssigkeiten ‐innovative Lösungsmittel (2001)

Abstract Salze, die wie Wasser bei Temperaturen unter 100 °C flüssig sind, bieten sich als alternative Reaktionsmedien zu organischen Lösungsmitteln an. Ziele einer nachhaltigen Chemie rücken mit diesen „ionischen Flüssigkeiten”︁ und ihren speziellen Eigenschaften näher.
Mixed-Backbone Oligonucleotides Containing Segments of Deoxynucleosides Phosphorothioate and 2'-O-Methylribonucleosides Methylphosphonate: Synthesis and Properties (1999)

Synthesis of mixed-backbone oligonucleotides containing segments of deoxynucleoside. phosphorothioate and 2'-O-methylribonucleoside methylphosphonate have been achieved by using N-Pent-4-enoyl (PNT) heterocyclic base-protected 2'-O-methylribonucleoside methylphosphonamidites. Use of PNT for heterocyclic base-protection allows the deprotection to be carried out under milder conditions without affecting base labile methylphosphonate internucleotide linkages. New MBOs have reduced phosphorothioate internucleotide linkages while maintaining affinity with target RNA and are stable towards nucleases.
A new system for evaluation of armrest use in robotic surgery and validation of a new ergonomic concept – armrest load (2016)

The armrest load score is a direct, sensitive measure for the ergonomic evaluation of a simulator's armrest use. This experience-dependent ergonomic difference between experts and novices (p = 0.007) highlights the importance of ergonomic training for novice robot users. Copyright © 2016 John Wiley & Sons, Ltd.
Formation behavior and refining approach of TiB2 particles synthesized by combustion reaction (2008)

Titanium boride (TiB2) particles were synthesized in aluminum matrix by a combustion reaction of Ti–B–Al preform, aiming at synthesizing nano-scale fine particles. The formation behavior of TiB2 particle was observed by Combustion Front Quenching Method (CFQM) , in which self-propagating combustion wave was terminated by heat absorption of metallic mold. At the earliest stage of the reaction, the reaction between aluminum and titanium took place, and boron was not involved in the reaction. The nucleation site of TiB2 was a peripheral area of boron particles. TiB2 particles synthesized at the early stage of the reaction was very fine (~200 nm) , and the growth of particles occurred during a high-temperature stage of the combustion reaction. The effect of powder blending ratio on the size of TiB2 particle was examined. The combustion temperature was reduced by increasing aluminum fraction in the preform. The synthesized TiB2 particle was effectively refined by increasing the blending ratio of aluminum. By using finer boron particles or by increasing boron fraction in the preform, TiB2 particle was also refined effectively.
Towards an understanding of the impact of autonomous path planning on victim search in USAR (2010)

Technology for multirobot systems has advanced to the point where we can consider their use in a variety of important domains, including urban search and rescue. A key to the practical usefulness of multirobot systems is the ability to have a large number of robots effectively controlled by small numbers of operators. In this paper, two modalities for controlling a team of 24 robots in a foraging task in an urban search and rescue environment are compared. In both modalities, multiple operators must monitor video streams from the robots to detect and mark victims on a map as well as teleoperating robots that cannot get themselves out of difficult situations. In the first modality, the operators must also provide waypoints for the robots to explore, using both video and a partially completed map to choose appropriate waypoints. In the second modality, the robots autonomously plan their paths, allowing operators to focus on monitoring the video, but without being able to interpret video streams to guide exploration. Experimental results show that significantly better overall performance is achieved with autonomous path planning, although the reduction in operator workload is not significant.
Scintillation properties of 2-inch-diameter Pr: Lu<inf>3</inf>A1<inf>5</inf>O<inf>12</inf> single crystal (2007)

Pr:LuAG has interesting properties of high density, high light yield and a very fast 5d-4f emission decay time. Recently we have develop 2-inch-diameter Pr:LuAG single crystal for scintillator applications such medical imaging and high-energy physics. In this report, we study uniformity of the light yield, energy resolution, decay time and gamma-ray response in the range from 59.5 keV ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am) to 1.4 MeV ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am).
A network modeling approach to elucidate drug resistance mechanisms and predict combinatorial drug treatments in breast cancer (2017)

The use of a logic-based, discrete dynamic model enables the identification of results that are mainly due to the organization of the signaling network, and those that also depend on the kinetics of individual events. Network-based models such as this will play an increasing role in the rational design of high-order therapeutic combinations.
Sesamolinol glucoside and other lignans from Sesame seeds with antimutagenic and lipid peroxidation inhibitory activities (2008)

Following our previous work on sesame testa [1], we applied a procedure based on XAD-4 adsorption resin, which permits the obtainment of an enriched polyphenolic extracts from Sesamum indicum seeds. Chemical analysis of the obtained extract led to the identification of twelve lignans. Among them, a new lignan, (+)-sesamolinol-4-O-β-D-glucoside (1), has been isolated and its structure determined by spectroscopic methods, mainly by the concerted application of 1D and 2D NMR techniques (HMQC, HMBC, NOESY) and mass spectroscopy. Some of the isolated compounds were evaluated for their antimutagenic and lipid peroxidation inhibitory activities.
Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn’s disease (2020)

Angiotensin-Converting Enzyme 2 ( <i>ACE2</i> ) has been identified as the host receptor for SARS-coronavirus 2 (SARS-CoV-2) which has infected millions world-wide and likely caused hundreds of thousands of deaths. Utilizing transcriptomic data from four cohorts taken from Crohn's disease (CD) and non-inflammatory bowel disease (IBD) subjects, we observed evidence of increased <i>ACE2</i> mRNA in ileum with demographic features that have been associated with poor outcomes in COVID-19 including age and raised BMI. <i>ACE2</i> was downregulated in CD compared to controls in independent cohorts. Within CD, <i>ACE2</i> expression was reduced in inflamed ileal tissue and also remarkably, from uninvolved tissue in patients with a worse prognosis in both adult and pediatric cohorts. In active CD, small bowel <i>ACE2</i> expression was restored by anti-TNF therapy particularly in anti-TNF responders. Collectively our data suggest that <i>ACE2</i> downregulation is associated with inflammation and worse outcomes in CD.
Specification for the Derivation of Root Keys from an Extended Master Session Key (EMSK) (2008)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements.
A 45-GHz SiGe HBT amplifier at greater than 25 % efficiency and 30 mW output power (2011)

An efficient power amplifier (PA) is demonstrated in a 0.12-μm silicon germanium (SiGe) BiCMOS process at 45 GHz. The amplifier is a single stage common-emitter amplifier (CE). The voltage handling capability of the amplifier is extended by a low impedance biasing network. The amplifier achieves a peak power-added efficiency (PAE) of 25 % at an output power of 13 dBm in linear operation and 31% in class B mode at an output power of 13.3 dBm. The maximum saturated output power P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> is 14.8 dBm, at which the circuit consumes 77 mW. The chip occupies an area of 0.27 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> including pads.
Behavioural difference of vascularized and non-vascularized retina after subretinal implantation of cellulose acetate membrane (2004)

Purpose: Age-related macular degeneration (ARMD) is the major reason of visual loss in elderly population. Main causes are loss of native retinal pigment epithel cells (RPE) and damaged Bruch's membrane. Resulting in subfoveal choriocapillaris atrophy [1] and loss of photoreceptors [2–4]. Pilot clinical trials have shown encouraging results transplanting cell suspensions of autologous RPE or iris PE [2, 5–9]. To assess the biocompatibility of porous cellulose acetate membrane as a substrate for transplanted cells and a replacement for Bruch's membrane, we used two distinct animal models with vascularized and non-vascularized retinae. Methods: Porous cellulose acetate membranes (80 µm and 30 µm thickness) with a molecular weight cut-off of 100 kD were selected due to their superior support of cultured cells in vitro. Membranes were implanted into the subretinal space of rabbits and pigs using a modified Grieshaber Cannulated Extrusion Needle. After one month in vivo, biocompatibility was assessed histologically. Results: In the non-vascularized rabbit model the membrane caused a diffuse loss of cells in overlying retina layers, while even directly adjacent parts of the the retina remained intact. In the vascularized pig model we found a loss of outer segments of the photoreceltors due to the missing RPE layer, but the overlying retina remained intact. Conclusion: Subretinal PE transplantation is a new and promising technique. Cellulose acetate membranes show a good biocompatibility and stability. In non-vascularized model minimal fibrotic reaction occured. Our results also demonstrate the the importance of the vascularized model.
Constructing deep-blue bis-tridentate Ir(iii) phosphors with fluorene-based dianionic chelates (2020)

Novel fluorene-based bis-tridentate Ir(<sc>iii</sc>) phosphors are capable of exhibiting both improved stability and efficient deep-blue emission in solution.