gebhart/patrepeval huggingface dataset:
Platinum Nanoparticles in Biomedicine: Preparation, Anti-Cancer Activity, and Drug Delivery Vehicles (2022)

Cancer is the main cause of morbidity and mortality worldwide, excluding infectious disease. Because of their lack of specificity in chemotherapy agents are used for cancer treatment, these agents have severe systemic side effects, and gradually lose their therapeutic effects because most cancers become multidrug resistant. Platinum nanoparticles (PtNPs) are relatively new agents that are being tested in cancer therapy. This review covers the various methods for the preparation and physicochemical characterization of PtNPs. PtNPs have been shown to possess some intrinsic anticancer activity, probably due to their antioxidant action, which slows tumor growth. Targeting ligands can be attached to functionalized metal PtNPs to improve their tumor targeting ability. PtNPs-based therapeutic systems can enable the controlled release of drugs, to improve the efficiency and reduce the side effects of cancer therapy. Pt-based materials play a key role in clinical research. Thus, the diagnostic and medical industries are exploring the possibility of using PtNPs as a next-generation anticancer therapeutic agent. Although, biologically prepared nanomaterials exhibit high efficacy with low concentrations, several factors still need to be considered for clinical use of PtNPs such as the source of raw materials, stability, solubility, the method of production, biodistribution, accumulation, controlled release, cell-specific targeting, and toxicological issues to human beings. The development of PtNPs as an anticancer agent is one of the most valuable approaches for cancer treatment. The future of PtNPs in biomedical applications holds great promise, especially in the area of disease diagnosis, early detection, cellular and deep tissue imaging, drug/gene delivery, as well as multifunctional therapeutics.
Caspase-mediated Cleavage of the Ubiquitin-protein Ligase Nedd4 during Apoptosis (1998)

The onset of apoptosis is coupled to the proteolytic activation of a family of cysteine proteases, termed caspases. These proteases cleave their target proteins after an aspartate residue. Following caspase activation during apoptosis, a number of specific proteins have been shown to be cleaved. Here we show that Nedd4, a ubiquitin-protein ligase containing multiple WW domains and a calcium/lipid-binding domain, is also cleaved during apoptosis induced by a variety of stimuli including Fas-ligation, gamma-radiation, tumor necrosis factor-alpha, C-8 ceramide, and etoposide treatment. Extracts from apoptotic cells also generated cleavage patterns similar to that seen in vivo, and this cleavage was inhibited by an inhibitor of caspase-3-like proteases. In vitro, Nedd4 was cleaved by a number of caspases, including caspase-1, -3, -6, and -7. By site-directed mutagenesis, one of the in vitro caspase cleavage sites in mouse Nedd4 was mapped to a DQPD237 downward arrow sequence, which is conserved between mouse, rat, and human proteins. This is the first report demonstrating that an enzyme of the ubiquitin pathway is cleaved by caspases during apoptosis.
Cobalt-Base Alloys for Biomedical Applications (1999)

Description STP 1365 is a unique publication that focuses on the use of cobalt-base alloys in orthopaedic applications. It features 18 peer-reviewed papers written by world renowned biomedical experts, that focus on new materials research, advanced process developments, accelerated wear studies, and clinical information related to the use of Co-26Cr-6Mo for surgical implant applications. STP 1365 covers the latest information to emerge in recent years on topics such as: • Alloy Design • Processing Variables • Corrosion/Fretting Resistance • Abrasion and Wear Characterization • Implant Surface Modification • Biological Response • Clinical Performance. This volume is a comprehensive resource for orthopaedic surgeons, biomedical researchers and engineers, product design engineers, quality control engineers, product metallurgists and managers, implant device manufacturers, and academics.
P016 Constitutive activity of the cation channel TRPM8 regulates monocyte to macrophage transition in humans to control intestinal inflammation (2019)

Abnormal intestinal monocyte to macrophage transition plays a critical role in inflammatory bowel disease (IBD). TRPM8 (Transient Receptor Potential Melastatin 8) is a ligand-gated cation channel activated by factors including cold and cooling compounds leading to cation influx. TRPM8 RNA is increased in both the colonic mucosa of Crohn’s disease patients and mice with experimentally induced colitis in which activation of TRPM8 with synthetic agonists ameliorates disease. Mice with TRPM8-deficient macrophages develop worse colitis, implying that TRPM8 in macrophages is protective against intestinal inflammation. Our aim was to test the hypothesis that TRPM8 activity controls inflammation in the human intestine by modulating monocyte to macrophage transition. Blood monocytes from healthy volunteers were differentiated into macrophages using M-CSF, in the presence or absence of TRPM8 antagonist (AMTB) or agonist (icilin). Intestinal CD14+ monocytes were extracted from colonic biopsies obtained from control patients. Flow cytometry was used to measure TRPM8 protein, membrane potential using DISBAC2(3) dye, phagocytosis of fluorescent microspheres, cell viability, and TNF-α production. RNA seq was used to determine differential gene expression. TRPM8 protein was detected in blood monocytes, in vitro derived macrophages and CD64+ monocyte/macrophages in the intestinal mucosa. Inhibition, but not activation of TRPM8 activity in blood monocytes resulted in membrane depolarisation after 3 h, which was associated with increased cell survival (p = 0.0001) and enhanced production of LPS-induced TNF-α (p = 0.0001, Figure 1) after 24 h. Inhibition of TRPM8 also enhanced TNF-α production by CD14+ intestinal monocytes. Macrophages generated from blood monocytes in the presence of AMTB had reduced phagocytic capacity (p = 0.03) and differential expression of 977 genes, indicating substantial effects on cell differentiation. Genes related to cell migration, including the gut homing integrin gene ITGB7, were decreased, whereas genes related to cytokine production were increased. Figure 1. Increased LPS-induced TNF-α production in CD14+ monocytes after culture with AMTB. TRPM8 is expressed in human blood and intestinal monocyte populations where it has constitutive activity that modulates the transition into macrophages and limits inflammation. Understanding alterations in this pathway in IBD may allow identification of novel therapeutic targets.
Abstract C147: Mechanism of resistance to a semisynthetic anticancer andrographolide derivative: Possible involvement of Ras-MAPK signaling pathway. (2013)

Abstract SRJ09 (3,19-(2-bromobenzylidene)andrographolide) has been identified as a lead anticancer agent on the basis of its selectivity towards breast and colon cancers in the USA NCI 60 cancer cell lines screen (Jada et al (2008) Br J Pharmacol, 155(5):641-54). In our recent seminal publication (Hocker et al (2013), PNAS, 110(25):10201-6), we revealed that the compound is a binder of oncogenic mutant K-Ras. In the present investigation, HCT116 colon cancer cells were made resistant to SRJ09 to elucidate the mechanism of resistance. MTT cell viability assay was utilized to screen for cross-resistance to other analogues of andrographolide (AGP) and standard anticancer drugs. Flow cytometry technique was utilized for cell cycle study. Western blot was performed to determine the expression of cell cycle, apoptosis regulatory and cell signaling proteins. Additionally, reverse transcriptase (RT)-PCR was carried out to determine the cell cycle regulatory genes. SRJ09-resistant HCT116 displayed approximately 40-fold resistance towards SRJ09 compared with the parental cells. However, the cells were not resistant towards AGP analogues and standard anticancer drugs. The cells failed to arrest in G1 phase upon treatment with SRJ09, unlike the parental cells. RT-PCR confirmed the findings that protein expression of p21 was not up-regulated and CDK4 was not down-regulated, contrary to the parental cells. The resistance of the cells to undergo apoptosis upon treatment with SRJ09 was mainly attributed to the unchanged levels of Bax, Bid, caspase 8 and 9, otherwise activated in the parental cells. The inability of the cells to experience cell cycle arrest and apoptosis might be attributed in part to the marginal changes in phosphorylated c-Raf and ERK1/2 protein levels, which are in complete contrast to the parental cells. In conclusion, the mechanism of resistance is very likely due to failure of c-Raf and ERK1/2 to undergo dephosphorylation, implicating Ras-MAPK pathway as a target of SRJ09. This study was funded by Universiti Putra Malaysia Research University Grant Scheme (04-01-09-0713RU; 04-02-12-2017RU). Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C147. Citation Format: Johnson Stanslas, Charng Choon Wong, Sreenivasa Rao Sagineedu, Shiran Sidik, Shariful Hasan Sumon, Roger Phillips, Nordin Haji Lajis. Mechanism of resistance to a semisynthetic anticancer andrographolide derivative: Possible involvement of Ras-MAPK signaling pathway. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C147.
Automatic speech recognition system channel modeling (2010)

In this paper, we present a systems approach for channel modeling of an Automatic Speech Recognition (ASR) system. This can have implications in improving speech recognition components, such as through discriminative language modeling. We simulate the ASR corruption using a phrase-based machine translation system trained between the reference phoneme and output phoneme sequences of a real ASR. We demonstrate that local optimization on the quality of phoneme-to-phoneme mappings does not directly translate to overall improvement of the entire model. However, we are still able to capitalize on contextual information of the phonemes which a simple acoustic distance model is not able to accomplish. Hence we show that the use of longer context results in a significantly improved model of the ASR channel.
The effect of sintering dopant incorporation in modified chemical vapor deposition (1989)

To determine the role of the diffusion of dopant (phosphorus, germanium, and fluorine) into silica particles and through the voids of porous soot during sintering, initially uniform soot layers are created with a stationary torch and then sintered at different rates, dopant partial pressures, and temperatures. The layer structure seen in modified chemical vapor deposition preforms is formed initially by gas phase thermal gradients during particle formation, but diffusion during sintering severely modifies the dopant level and slightly increases the concentration gradient within each layer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High symbol rate transmission systems for data rates above 400 Gb/s using ETDM transmitters and receivers (2014)

We review high-speed experimental coherent transmission systems for bit rates from 400 Gb/s to 1.2 Tb/s, using high-speed electronic multiplexing to symbol rates from 72 GBd to 107 GBd.
Total variation minimization for in-beam PET image reconstruction (2012)

One of the challenging applications of positron emission tomography (PET) is in-beam PET, which is an in situ dose monitoring method for charged particle therapy. It is known that the activity of positron emitters produced through fragmentation reaction is generally low. Image reconstruction from low count data would require alternative algorithms to suppress noise in images, such as the maximum a posteriori (MAP) reconstruction algorithm, which is often used to improve an image reconstruction problem by introducing penalty functions. In particular, the total variation (TV) norm has been proposed as a penalty function to suppress noise while preserving edges. In this study, we applied a MAP-TV image reconstruction algorithm to in-beam PET imaging, and we evaluated the effect of TV constraint for the in-beam PET image in terms of detection performance of distal edge a of positron emitter distribution along beam irradiation. We applied the one-step-Iate algorithm combined with the TV norm to a new small prototype of the single-ring OpenPET (SROP), which is our second generation OpenPET geometry. The small SROP prototype consisted of two oval detector rings which were slanted by 45 degree and stacked. We carried out initial in-beam experiments in the Heavy Ion Medical Accelerator in Chiba (HIMAC). In the experiment, we used a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> C beam. The target was a rectangular parallelepiped phantom (40 × 40 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 100 mm long) made of polymethyl methacrylate (PMMA). We calculated averaged peak position of profiles obtained in reconstructed images. In the experimental results, reconstructed images became smoother and less noisy with stronger constraint. It was shown that the MAP-TV algorithm enables smoothness and less noisy in reconstructed images even from the low count.
Additional file 9: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus (2017)

Organic acid production. (XLSX 40 kb)
Author Correction: Comparative and demographic analysis of orang-utan genomes (2022)

In this Article, we reported genome sequencing data from five Sumatran and five Bornean orang-utans. In re-analysing these data, Banes et al.1 found that eight of the ten samples were mislabelled, and we wish to correct the original publication according to their findings. In addition, Banes et al.1 find that one of the orang-utans that we had labelled as a male Sumatran is in fact a female Tapanuli orang-utan (an orang-utan species that was unknown at the time of publication of our original Article and that was first reported in 2017 (ref. 2)). While we here correct the original tables to display the correct names and IDs of the individuals studied, we do not correct the analyses in the original paper since the Tapanuli species was discovered only after we had concluded our study. We refer the reader to Banes et al.1 for further information. In the main text, the sentence “We also sequenced the genomes of 10 additional unrelated wild-caught orang-utans, five Sumatran and five Bornean, using a short read sequencing platform (297 Gb of data in total; Supplementary Information section 4)” should have read “We also sequenced the genomes of 10 additional unrelated wild-caught orang-utans, four Sumatran, five Bornean and one Tapanuli, using a short read sequencing platform (297 Gb of data in total; Supplementary Information section 4)”. In addition, the sentence “We then called single nucleotide polymorphisms (SNPs) from the alignment of all short read data from 10 individuals (five Bornean, including the 20-fold coverage mentioned above, and five Sumatran) (Supplementary Information section 4)” should have read “We then called single nucleotide polymorphisms (SNPs) from the alignment of all short read data from 10 individuals (five Bornean, including the 20-fold coverage mentioned above, four Sumatran and one Tapanuli) (Supplementary Information section 4).
Comparative Case Series of Exostoses and Osteomas of the Internal Auditory Canal (2011)

Exostoses and osteomas are benign bony lesions of the auditory canal. Although common in the external auditory canal, they are rare and difficult to distinguish in the internal auditory canal (IAC). In this literature review and case presentation, we define radiologic and histologic criteria to differentiate exostoses from osteomas of the IAC. Two patients with exostoses and 1 patient with an osteoma of the IAC are described here. Patient 1 presented with disabling vertigo and was found to have bilateral exostoses with nerve impingement on the right. After removal of the right-sided exostoses via retrosigmoid craniotomy, the patient had complete resolution of her symptoms over 1 year. Patient 2 presented with bilateral pulsatile tinnitus and vertigo and was found to have bilateral IAC exostoses. Patient 3 presented with hearing loss and tinnitus, and a unilateral IAC osteoma was ultimately discovered. Because of the mild nature of their symptoms, patients 2 and 3 were managed without surgery. We show that IAC osteomas can be differentiated from exostoses by radiographic evidence of bone marrow in high-resolution computed tomography scans, or by the presence of fibrovascular channels on histologic analysis. Management of these rare entities is customized on the basis of patient symptoms.
Photoacoustic topography through an ergodic relay for functional imaging and biometric application in vivo (2020)

PATER has achieved a high-speed temporal resolution over a large field of view. Our results suggest that PATER is a promising and economical alternative to PACT for fast imaging.
Tools for expressive text-to-speech markup (2001)

This paper describes handicapped accessible text-to-speech markup software developed for poetry and performance. Most text-to-speech software allows the user to select a voice, but provides no control over performance parameters such as rate, volume, and pitch. For users with vocal disabilities, the default "computer voice" is often dreaded since it provides no personalization. Evolving standards exist for text-to-speech markup (Sable, Java Speech Markup Language, Spoken Text Markup Language), but few tools exist for non-experts to modify documents using these prosody options [1, 5]. Furthermore, we could find fewer tools allowing for straightforward live performance using a synthesized voice [3]. Thus we created an easy to learn text-to-speech markup tool that requires little training to use.
Rv2131c fromMycobacterium tuberculosisIs a CysQ 3′-Phosphoadenosine-5′-phosphatase (2008)

Mycobacterium tuberculosis ( Mtb) produces a number of sulfur-containing metabolites that contribute to its pathogenesis and ability to survive in the host. These metabolites are products of the sulfate assimilation pathway. CysQ, a 3'-phosphoadenosine-5'-phosphatase, is considered an important regulator of this pathway in plants, yeast, and other bacteria. By controlling the pools of 3'-phosphoadenosine 5'-phosphate (PAP) and 3'-phosphoadenosine 5'-phosphosulfate (PAPS), CysQ has the potential to modulate flux in the biosynthesis of essential sulfur-containing metabolites. Bioinformatic analysis of the Mtb genome suggests the presence of a CysQ homologue encoded by the gene Rv2131c. However, a recent biochemical study assigned the protein's function as a class IV fructose-1,6-bisphosphatase. In the present study, we expressed Rv2131c heterologously and found that the protein dephosphorylates PAP in a magnesium-dependent manner, with optimal activity observed between pH 8.5 and pH 9.5 using 0.5 mM MgCl 2. A sensitive electrospray ionization mass spectrometry-based assay was used to extract the kinetic parameters for PAP, revealing a K m (8.1 +/- 3.1 microM) and k cat (5.4 +/- 1.1 s (-1)) comparable to those reported for other CysQ enzymes. The second-order rate constant for PAP was determined to be over 3 orders of magnitude greater than those determined for myo-inositol 1-phosphate (IMP) and fructose 1,6-bisphosphate (FBP), previously considered to be the primary substrates of this enzyme. Moreover, the ability of the Rv2131c-encoded enzyme to dephosphorylate PAP and PAPS in vivo was confirmed by functional complementation of an Escherichia coli Delta cysQ mutant. Taken together, these studies indicate that Rv2131c encodes a CysQ enzyme that may play a role in mycobacterial sulfur metabolism.
Heart Failure and Multimorbidity in Asia (2023)

Asian patients with HF are almost a decade younger than Western Europe and North American patients. However, over two in three patients have multimorbidity. Comorbidities usually cluster due to the close and complex links between chronic medical conditions. Elucidating these links may guide public health policies to address risk factors. In Asia, barriers in treating comorbidities at the patient, healthcare system and national level hamper preventative efforts. Asian patients with HF are younger yet have a higher burden of comorbidities than Western patients. A better understanding of the unique co-occurrence of medical conditions in Asia can improve the prevention and treatment of HF.
Modeling of antenna geometry and thickness optimization for wideband UHF RFID tag (2015)

In this paper, we present a novel design for wideband Ultra High Frequency (UHF) Radio Frequency Identification (RFID) passive tag. The optimized design has compact size and covers all the bandwidth for global UHF RFID (860MHz–960MHz). For flexible customization in real-world applications, an equivalent model of antenna geometry is also proposed in this work. The agreement between equivalent model with lumped elements and 3D EM simulation of antenna geometry in 2 different simulator (ADS and CST Microwave Studio) proves the feasibility of design in practical applications. Furthermore, we executed also the optimization of antenna thickness in order to reduce the price of commercial tags. From experimental results, the good agreement between simulation and measurement proves the feasibility of equivalent model and the repeatability of fabrication process. The optimized design has the acceptable read-range (over 8m) in all the bandwidth of global UHF RFID and optimized thickness for antenna should be between 5-μm and 6-μm to keep the good performance of fabricated RFID tags.
Towards a Fully Printable Battery: Robocast Deposition of LiFePO4 Cathode Structures (2009)

Abstract not Available.
Optimizing Replication, Communication, and Capacity Allocation in CMPs (2005)

Chip multiprocessors substantially increase capacity pressure on the on-chip memory hierarchy while requiring fast access. Neither private nor shared caches can provide both large capacity and fast access in CMPs. We observe that compared to symmetric multiprocessors (SMPs), CMPs change the latency capacity tradeoff in two significant ways. We propose three novel ideas to exploit the changes: (1) Through placing copies close to requestors allows fast access for read-only sharing, the copies also reduce the already-limited on-chip capacity in CMPs. We propose controlled replication to reduce capacity pressure by not making extra copies in some cases, and obtaining the data from an existing on-chip copy. This option is not suitable for SMPs because obtaining data from another processor is expensive and capacity is not limited to on-chip storage. (2) Unlike SMPs, CMPs allow fast on-chip communication between processors for read-write sharing. Instead of incurring slow access to read-write shared data through coherence misses as do SMPs, we propose in situ communication to provide fast access without making copies or incurring coherence misses. (3) Accessing neighbor's caches is not as expensive in CMPs as it is in SMPs. We propose capacity stealing in which private data that exceeds a core's capacity is placed in a neighboring cache with less capacity demand. To incorporate our ideas, we use a hybrid of private, per-processor tag arrays and a shared data array. Because the shared data is slow, we employ non-uniform access and distance associativity from previous proposals to hold frequently-accessed data in regions close to the requestor. We extend the previously-proposed non-uniform access with replacement and placement using distance associativity (NuRAPID) ro CMPs, and call our cache CMP-NuRAPID. Our result show that for a 4-core CMP with 8 MB cache, CMP-NuRAPID improves performance by 13% over a shared cache and 8% over private caches for three commercial multithreaded workloads.