gebhart/patrepeval huggingface dataset:
Enterolactone induces apoptosis in human prostate carcinoma LNCaP cells via a mitochondrial-mediated, caspase-dependent pathway (2007)

The mammalian lignan enterolactone is a major metabolite of plant-based lignans that has been shown to inhibit the growth and development of prostate cancer. However, little is known about the mechanistic basis for its anticancer activity. In this study, we report that enterolactone selectively suppresses the growth of LNCaP prostate cancer cells by triggering apoptosis. Mechanistic studies showed that enterolactone-induced apoptosis was characterized by a dose-dependent loss of mitochondrial membrane potential, release of cytochrome c and cleavage of procaspase-3 and poly(ADP-ribose)-polymerase (PARP). Caspase dependence was indicated by the ability of the pan-caspase inhibitor z-VAD-fmk to attenuate enterolactone-mediated apoptosis. Mechanistic studies suggested roles for Akt, GSK-3beta, MDM2, and p53 in enterolactone-dependent apoptosis. Our findings encourage further studies of enterolactone as a promising chemopreventive agent against prostate cancer.
Wire-Arc Spraying Of Metal Onto Insulating Foam (1995)

Wire-arc spraying used to deposit protective metallic coats on thermally insulating foams. Process relatively fast and cheap, and does not damage foam or involve toxic and polluting chemicals.
Nucleic acid purification from plants, animals and microbes in under 30 seconds (2017)

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.
<sup>18</sup>F-FDG PET/CT for Monitoring of Treatment Response in Breast Cancer (2016)

Changes in tumor metabolic activity have been shown to be an early indicator of treatment effectiveness for breast cancer, mainly in the neoadjuvant setting. The histopathologic response at the completion of chemotherapy has been used as the reference standard for assessment of the accuracy of (18)F-FDG PET in predicting a response during systemic treatment. Although a pathologic complete response (pCR) remains an important positive prognostic factor for an individual patient, a recent metaanalysis could validate pCR as a surrogate marker for patient outcomes only in aggressive breast cancer subtypes. For establishment of the clinical application of metabolic treatment response studies, larger series of specific breast cancer subtypes-including hormone receptor-positive, human epidermal growth factor receptor 2-positive, and triple-negative breast cancers-are necessary. In addition, thresholds for relative changes in (18)F-FDG uptake to distinguish between responding and nonresponding tumors need to be validated for different systemic treatment approaches, with progression-free survival and overall survival as references. A PET-based treatment stratification is applicable clinically only if valid alternative therapies are available. Of note, patients who do not achieve a pCR might still benefit from neoadjuvant therapy enabling breast-conserving surgery. In the metastatic setting, residual tumor metabolic activity after the initiation of systemic therapy is an indicator of active disease, whereas a complete resolution of metabolic activity is predictive of a successful treatment response.
Calculation of Transport Coefficient Profiles in Modulation Experiments as an Inverse Problem (2012)

The calculation of transport profiles from experimental measurements belongs in the category of inverse problems which are known to come with issues of ill-conditioning or singularity. A reformulation of the calculation, the matricial approach, is proposed for periodically modulated experiments, within the context of the standard advection-diffusion model where these issues are related to the vanishing of the determinant of a 2×2 matrix. This sheds light on the accuracy of calculations with transport codes, and provides a path for a more precise assessment of the profiles and of the related uncertainty.
A Toxicologic Review of Quantum Dots: Toxicity Depends on Physicochemical and Environmental Factors (2005)

As a growing applied science, nanotechnology has considerable global socioeconomic value, and the benefits afforded by nanoscale materials and processes are expected to have significant impacts on almost all industries and all areas of society. A diverse array of engineered nanoscale products and processes have emerged [e.g., carbon nanotubes, fullerene derivatives, and quantum dots (QDs)], with widespread applications in fields such as medicine, plastics, energy, electronics, and aerospace. With the nanotechnology economy estimated to be valued at dollar 1 trillion by 2012, the prevalence of these materials in society will be increasing, as will the likelihood of exposures. Importantly, the vastness and novelty of the nanotechnology frontier leave many areas unexplored, or underexplored, such as the potential adverse human health effects resulting from exposure to novel nanomaterials. It is within this context that the need for understanding the potentially harmful side effects of these materials becomes clear. The reviewed literature suggests several key points: Not all QDs are alike; engineered QDs cannot be considered a uniform group of substances. QD absorption, distribution, metabolism, excretion, and toxicity depend on multiple factors derived from both inherent physicochemical properties and environmental conditions; QD size, charge, concentration, outer coating bioactivity (capping material and functional groups), and oxidative, photolytic, and mechanical stability have each been implicated as determining factors in QD toxicity. Although they offer potentially invaluable societal benefits such as drug targeting and in vivo biomedical imaging, QDs may also pose risks to human health and the environment under certain conditions. Key words: environment, human health, nanomaterials, nanosized particles, nanotechnology, nanotoxicology, quantum dots, toxicology.
Rate-Compatible Puncturing of Low-Density Parity-Check Codes (2004)

In this correspondence, we consider puncturing of low-density parity-check (LDPC) codes for additive white Gaussian noise (AWGN) channels. We show that good puncturing patterns exist and that the puncturing can be performed in a rate-compatible fashion. Furthermore, rate-compatible puncturing results in a small loss of performance with respect to threshold, namely, the punctured code is good (in terms of threshold) across a range of rates when compared with the optimal codes for each rate. This allows one to implement a single "mother" encoder and decoder that is good across a wide range of rates.
Study of Parameters and Theory of Sucrose Dust Explosion (2022)

To investigate the parameters of sucrose dust explosion, the minimum ignition energy (MIE) and minimum ignition temperature (MIT) were evaluated. The experiments tested the MIE of sucrose dust under different conditions of dust quantity, ignition delay time (IDT), and powder injection pressure (PIP). The experiments tested the MIT of different particle sizes. The results demonstrate that the MIE of sucrose powder under three conditions was an open-up quadratic polynomial. When the dust quantity, the IDT, and PIP were 0.5 g (417 g/m3), 90 ms, and 150 kPa, respectively, the MIE was 58.9 mJ, 62.6 mJ, and 52.4 mJ. The MIT was positively correlated with the particle size of sucrose dust, and the MIT was 340 °C. At the molecular level, the “O–H” bonds of the sucrose molecule hydroxyl groups were broken by the discharge of electrodes or high temperature to generate H2. The combustion of H2 caused the explosion to spread to the surrounding sucrose dust and made the deposited dust rise, forming an interlocking explosion. The explosion would not stop until the dust concentration dropped below the lowest explosion limit. The results of this study can provide guidance for sucrose enterprises to prevent dust explosion accidents.
The low density lipoprotein receptor. Identification of amino acids in cytoplasmic domain required for rapid endocytosis. (1987)

The 50-residue cytoplasmic domain of the low density lipoprotein receptor (amino acids 790-839) directs the receptor to coated pits, thereby facilitating rapid endocytosis of bound low density lipoprotein. To determine the structural features required for this targeting, we produced 24 mutations in the cytoplasmic domain through use of oligonucleotide-directed mutagenesis. The first 22 amino acids of the cytoplasmic domain (residues 790-811) are sufficient for rapid internalization. The amino acid at position 807 is especially critical. Aromatic residues (tyrosine, phenylalanine, or tryptophan) at this position allow rapid internalization. Charged or uncharged aliphatic residues do not substitute. Although the requirements at the neighboring positions (806 and 808) are less stringent, the insertion of proline at position 806 is detrimental. These specificities suggest that the juxtamembranous region of the cytoplasmic domain participates in protein:protein interactions that allow the low density lipoprotein receptor to cluster in coated pits.
On Reduction of Cavitation Noise and Pressure Fluctuation Induced by a Cavitating Propeller due to Air Injection (1988)

In this paper, extensive experiments are described on pressure fluctuations and cavitation noise induced by a cavitating propeller working behind a complete ship model. Model of a conventional propeller and a highly skewed propeller both of which have injection holes near the leading edge, were used to determine the effect of air injection on sheet cavitation noise and pressure fluctuation, and to demonstrate the flow field on an unsteady propeller blade. The experiments were conducted without air injection and with air injected at different air flow rates. The results show that the injection of air into the cavity reduces cavitation noise by about 20 dB maximum. Little effect on pressure fluctuation and cavitation extent was observed. As the air flow rate increased from 04 liter/min, cavitation noise was reduced, but above 4 liter/min there was no further reduction. In this measurement, sophisticated experimental techniques were used to obtain significant data on cavitation extent, pressure fluctuations and noise in a cavitation tunnel. These were the wake simulation technique using flow liners and artificial nuclei seeding.
Avoiding unconditional jumps by code replication (1992)

This study evaluates a global optimization technique that avoids unconditional jumps by replicating code. When implemented in the back-end of an optimizing compiler, this technique can be generalized to work on almost all instances of unconditional jumps, including those generated from conditional statements and unstructured loops. The replication method is based on the idea of finding a replacement for each unconditional jump which minimizes the growth in code size. This is achieved by choosing the shortest sequence of instructions as a replacement. Measurements taken from a variety of programs showed that not only the number of executed instructions decreased, but also that the total cache work was reduced (except for small caches) despite increases in code size. Pipelined and superscalar machines may also benefit from an increase in the average basic block size.
Identification of Surprisingly Diverse Type IV Pili, across a Broad Range of Gram-Positive Bacteria (2011)

We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins.
On packet lengths and overhead for random linear coding over the erasure channel (2007)

We assess the practicality of random network coding by illuminating the issue of overhead and considering it in conjunction with increasingly long packets sent over the erasure channel. We show that the transmission of increasingly long packets, consisting of either of an increasing number of symbols per packet or an increasing symbol alphabet size, results in a data rate approaching zero over the erasure channel. This result is due to an erasure probability that increases with packet length. Numerical results for a particular modulation scheme demonstrate a data rate of approximately zero for a large, but finite-length packet. Our results suggest a reduction in the performance gains offered by random network coding.
Image Classification using AlexNet with SVM Classifier and Transfer Learning (2019)

Since the last decade, Deep Learning has paved the direction for demanding and wide-ranging applications in almost everyday life and attained quite good performance on a diversity of complex problems such as face recognition, motion detection, health informatics and many more. This paper discusses the performance of state-of-the-art pre-trained Convolutional Neural Networks (CNNs) model. We have analyzed the accuracy and training time of AlexNet (already trained on millions of images) while using it with Support Vector Machines (SVM) classifier and under Transfer Learning (TL). Since training CNN from scratch is time-consuming in case of real problems and is compute-intensive so the image features extraction using already trained AlexNet network reduces effort and computation resources. The learned features are used to train a supervised SVM classifier and transfer learning (fine-tuning) of layers is achieved by retraining in the last few layers of pretrained network for image classification. The classification accuracy while Transfer Learning is obtained greater and more stable than SVM classifier.
PixMatch: Unsupervised Domain Adaptation via Pixelwise Consistency Training (2021)

Unsupervised domain adaptation is a promising technique for semantic segmentation and other computer vision tasks for which large-scale data annotation is costly and time-consuming. In semantic segmentation, it is attractive to train models on annotated images from a simulated (source) domain and deploy them on real (target) domains. In this work, we present a novel framework for unsupervised domain adaptation based on the notion of target-domain consistency training. Intuitively, our work is based on the idea that in order to perform well on the target domain, a model’s output should be consistent with respect to small perturbations of inputs in the target domain. Specifically, we introduce a new loss term to enforce pixelwise consistency between the model’s predictions on a target image and a perturbed version of the same image. In comparison to popular adversarial adaptation methods, our approach is simpler, easier to implement, and more memory-efficient during training. Experiments and extensive ablation studies demonstrate that our simple approach achieves remarkably strong results on two challenging synthetic-to-real benchmarks, GTA5-to-Cityscapes and SYNTHIA-to-Cityscapes.
The Immune Receptor Roq1 Confers Resistance to the Bacterial Pathogens Xanthomonas, Pseudomonas syringae, and Ralstonia in Tomato (2020)

<i>Xanthomonas</i> species, <i>Pseudomonas syringae</i> and <i>Ralstonia</i> species are bacterial plant pathogens that cause significant yield loss in many crop species. Generating disease-resistant crop varieties can provide a more sustainable solution to control yield loss compared to chemical methods. Plant immune receptors encoded by nucleotide-binding, leucine-rich repeat (NLR) genes typically confer resistance to pathogens that produce a cognate elicitor, often an effector protein secreted by the pathogen to promote virulence. The diverse sequence and presence/absence variation of pathogen effector proteins within and between pathogen species usually limits the utility of a single NLR gene to protecting a plant from a single pathogen species or particular strains. The NLR protein Recognition of XopQ 1 (Roq1) was recently identified from the plant <i>Nicotiana benthamiana</i> and mediates perception of the effector proteins XopQ and HopQ1 from <i>Xanthomonas</i> and <i>P. syringae</i> respectively. Unlike most recognized effectors, alleles of XopQ/HopQ1 are highly conserved and present in most plant pathogenic strains of <i>Xanthomonas</i> and <i>P. syringae</i>. A homolog of XopQ/HopQ1, named RipB, is present in most <i>Ralstonia</i> strains. We found that Roq1 confers immunity to <i>Xanthomonas</i>, <i>P. syringae</i>, and <i>Ralstonia</i> when expressed in tomato. Strong resistance to <i>Xanthomonas perforans</i> was observed in three seasons of field trials with both natural and artificial inoculation. The <i>Roq1</i> gene can therefore be used to provide safe, economical, and effective control of these pathogens in tomato and other crop species and reduce or eliminate the need for traditional chemical controls.
Preparation, Phytochemical Investigation, and Safety Evaluation of Chlorogenic Acid Products from Eupatorium adenophorum (2016)

<i>Eupatorium adenophorum</i> is widely distributed throughout the world's tropical and temperate regions. It has become a harmful weed of crops and natural environments. Its leaves contain bioactive compounds such as chlorogenic acid and may be used as feed additives. In this study, chlorogenic acid was extracted and separated from leaves of <i>E. adenophorum</i>. Three chlorogenic acid products were prepared with different purities of 6.11%, 22.17%, and 96.03%. Phytochemical analysis demonstrated that the main toxins of sesquiterpenes were almost completely removed in sample preparation procedure. The three products were evaluated for safety via in vitro and in vivo toxicological studies. All the products exhibited no cytotoxic effects at a dose of 400 μg/mL in an in vitro cell viability assay. When administered in vivo at a single dose up to 1.5 g/kg bw, all three products caused no signs or symptoms of toxicity in mice. These results encourage further exploration of extracts from <i>E. adenophorum</i> in feed additive application.
Bioimaging analysis of nuclear factor‐κB activity in Philadelphia chromosome‐positive acute lymphoblastic leukemia cells reveals its synergistic upregulation by tumor necrosis factor‐α‐stimulated changes to the microenvironment (2011)

To gain an insight into the microenvironmental regulation of nuclear factor (NF)-κB activity in the progression of leukemia, we established a bioluminescent imaging model of Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) cells transduced with a NF-κB/luciferase (Luc) reporter and cocultured with murine stromal cells and cytokines. Stromal cells alone did not augment Luc activity, taken as an index of NF-κB, but Luc activity was synergistically upregulated by the combination of stromal cells and tumor necrosis factor (TNF)-α. Dehydroxymethylepoxyquinomicin (DHMEQ), a specific inhibitor of NF-κB DNA binding, rapidly induced the apoptosis of Ph+ALL cells, indicating that NF-κB is necessary for the growth and survival of these cells. However, the DHMEQ-induced suppression of NF-κB activity and the apoptosis of leukemia cells were attenuated by the presence of stromal cells and TNF-α. In NOD-SCID mice transplanted with NF-κB/Luc reporter-containing Ph+ALL cell lines and monitored periodically during the progression of the leukemia, murine TNF-α was significantly expressed in lesions in which the leukemia cells emitted a significant NF-κB signal. These results support the notion that TNF-α also triggers microenvironmental upregulation of NF-κB activity in vivo. Collectively, the results indicated that TNF-α-stimulated microenvironment may contribute to the survival and progression of Ph+ALL cells through the synergistic upregulation of NF-κB activity.
Effective Segmentation based on Vocal Effort Change Point Detection 1 (2008)

Non-neutral speech data has a strong negative impact on speech processing systems such as Automatic Speech Recognition (ASR) or speaker ID systems [1]. It is therefore necessary to detect and segment non-neutral speech data before further processing steps. Alternatively, the detection and segmentation of non-neutral speech segments from an input speech stream can be used in speech analysis and understanding, or in speech file retrieval systems to detect speech files containing whispered speech representing sensitive information, or shouted speech denoting strong emotion. This study addresses the segmentation problem for vocal effort change by deploying an improved feature based T 2 -BIC algorithm. Several features are considered as input to the T 2 -BIC algorithm in this study. A new fused evaluation criterion, Multi-Error Score (MES), is proposed to explore which feature conveys the most information on vocal effort. Results show that the lowest mean MES (56.49) occurs for the energy ratio feature for segmentation of different vocal effort speech segments based on vocal effort change point detection. Finally, recommendations are made for integrating this framework to advance knowledge processing for subsequent speech systems. Index Terms: Segmentation, vocal effort, change point detection, whispered speech, shouted speech, T 2 -BIC
Content-addressable-memory-based single-stage optical modified-signed-digit arithmetic (1989)

Using a novel nonholographic optoelectronic content-addressable memory in a free-space angular multiplexing geometry, a single-optical-stage compact parallel optical modified-signed-digit arithmetic processing architecture is proposed. Some spatial light modulator based experimental results are also presented.