gebhart/patrepeval huggingface dataset:
Upper‐Room Ultraviolet Germicidal Irradiation (UVGI) for Air Disinfection: A Symposium in Print (2013)

Upper-room ultraviolet germicidal irradiation (UVGI) has several applications, its most important use is to reduce tuberculosis transmission in high-burden, resource-limited settings, especially those dealing with epidemics of drug-resistant disease. The efficacy of upper-room (UVGI) to reduce the transmission of airborne infection in real-world settings is no longer in question. International application (dosing) guidelines are needed, as are safety standards and commissioning procedures. A recent symposium to build consensus on guidelines discussed specifications for affordable UVGI fixture designs, safety, performance, computer-aided design (CAD) for UVGI, maintenance, dosimetry, gonioradiometric measurement and innovation using germicidal LEDs.
Diphone synthesis for phonetic vocoding (2005)

We report on the synthesis of speech in the context of a phonetic vocoder operating at 100 b/s. With each phoneme, the vocoder transmits the duration and a single pitch value. The synthesizer uses a large inventory of diphone "models" to synthesize a desired phoneme string. The diphone inventory has been selected to differentiate between prevocalic and postvocalic allophones of sonorants, to account for changes in vowel color conditioned by postvocalic liquids, to allow exact specification of voice onset time, and to permit synthesis of glottal stops alveolar flaps and syllabic consonants. The diphones are extracted from carefully constructed short utterances and are stored as a sequence of LPC parameters. During synthesis, the requisite diphone models are time-warped, abutted and smoothed to produce a complete sequence of LPC parameters that are used in the synthesis. The algorithms used are described and compared with more conventional methods. Examples of the synthesized speech will be played.
User clusters based hierarchical cooperative spectrum sensing in cognitive radio networks (2009)

This paper investigates secondary user clusters based cooperative spectrum sensing. Secondary users in the cognitive radio network are grouped into multiple clusters and the cooperative spectrum sensing is performed on a hierarchical architecture of these user clusters, through two levels of user collaborations. The low level cooperation is carried out within each cluster while the high level one is accomplished inside the cluster of the clusterheads. We propose soft fusion and hard fusion according to the bandwidth constraints of the control channels and the spectrum sensing agility requirement. An optimal soft fusion scheme and a double-threshold strategy are proposed to improve the overall spectrum sensing performance in soft fusion and hard fusion, respectively. Analysis and simulations verify that the proposed hierarchical cooperative spectrum sensing schemes can significantly improve the spectrum sensing performance.
Physiological Effects of Physical Postharvest Treatments on Insects (2003)

As concerns about the safety of our food supply increase along with concerns about the impact of agricultural chemicals on our environment, the development of nonchemical quarantine treatments to meet export requirements become increasingly necessary. The types of physical treatments used have been largely determined by commodity tolerances and processing practices. The most common physical treatments use temperature extremes such as heat [>40 °C (104.0 °F)] and cold [<10 °C (50.0 °F)]. Other physical treatments commonly include the use of controlled or modified atmospheres (low oxygen, elevated carbon dioxide). Current technology has led to investigations in the application of energy to control infesting insects. These treatments include ionizing radiation, microwaves, ultraviolet radiation, infrared radiation, radio frequency, electron beam, X-rays, and electricity. Although the effects of these physical treatments can impact commodity quality, the goal of the treatments is to kill infesting (real or in certain instances, potential) insects to meet quarantine requirements. The effects of physical treatments on insect mortality and fecundity are discussed.
Cross-linked beta alumina nanowires with compact gel polymer electrolyte coating for ultra-stable sodium metal battery (2019)

Abstract Sodium metal batteries have potentially high energy densities, but severe sodium-dendrite growth and side reactions prevent their practical applications, especially at high temperatures. Herein, we design an inorganic ionic conductor/gel polymer electrolyte composite, where uniformly cross-linked beta alumina nanowires are compactly coated by a poly(vinylidene fluoride-co-hexafluoropropylene)-based gel polymer electrolyte through their strong molecular interactions. These beta alumina nanowires combined with the gel polymer layer create dense and homogeneous solid-liquid hybrid sodium-ion transportation channels through and along the nanowires, which promote uniform sodium deposition and formation of a stable and flat solid electrolyte interface on the sodium metal anode. Side reactions between the sodium metal and liquid electrolyte, as well as sodium dendrite formation, are successfully suppressed, especially at 60 °C. The sodium vanadium phosphate/sodium full cells with composite electrolyte exhibit 95.3% and 78.8% capacity retention after 1000 cycles at 1 C at 25 °C and 60 °C, respectively.
DS-8201a, a HER2-targeting antibody-drug conjugate, to elicit immune responses and benefits in combination with an anti-PD-1 antibody. (2017)

1031 Background: DS-8201a, a HER2-targeting antibody–drug conjugate (ADC), with a topoisomerase I inhibitor, exatecan drivative (DX-8951 derivative, DXd) has been shown to have antitumor effects in preclinical xenograft models and clinical trials, but the involvement of the immune system in the antitumor efficacy of DS-8201a has not been elucidated yet. Methods: The antitumor efficacy of DS-8201a individually and in combination with an anti-PD-1 antibody was determined in a syngeneic mouse model with human HER2-expressing CT26.WT (CT26.WT-hHER2) cells. Mice whose tumors had been cured by DS-8201a treatment were rechallenged with CT26.WT-hHER2 cells; their splenocytes were co-cultured with CT26.WT-hHER2 or CT26.WT-mock cells, and IFN-g secretion by these cells was determined. To investigate effects of DXd and DS-8201a on dendritic cells (DCs), the expression of DC markers on bone marrow derived DCs (BMDCs) and intratumoral DCs was analyzed by flow cytometry. Furthermore, MHC class I and PD-L1 expression on tumor cells was analyzed. Results: At a weekly dosage of 10 mg/kg, DS-8201a showed significant antitumor effects in the mouse model. Mice whose tumors had been cured by DS-8201a treatment rejected the rechallenge with CT26.WT-hHER2 cells, and splenocytes from these mice were activated by both CT26.WT-hHER2 and CT26.WT-mock cells. In the mouse model, DS-8201a treatment raised a population of intratumoral DCs (CD45 + CD11c + MHC class II + ) and increased DC expression of CD86, a DC activation marker; DXd also up-regulated CD86 expression on BMDCs in vitro. Furthermore, DS-8201a up-regulated PD-L1 and MHC class I expression on tumor cells. Notably, antitumor effects of the combination of DS-8201a with an anti-PD-1 antibody were better than those of monotherapy. Conclusions: DS-8201a elicits immune responses via mechanisms other than cytotoxic effects on tumor cells. This finding suggests additional benefits of combining DS-8201a with an immune checkpoint inhibitor (ICI). The combination of DS-8201a and an anti-PD-1 antibody was effective in tumor suppression, indicating that DS-8201a may be successfully combined with an ICI in human clinical applications.
Phosphoinositol lipids bind to phosphatidylinositol 3 (PI3)-kinase enhancer GTPase and mediate its stimulatory effect on PI3-kinase and Akt signalings (2005)

Phosphatidylinositol 3 (PI3)-kinase enhancer (PIKE) is a nuclear GTPase that enhances PI3-kinase activity in a GTP-dependent manner. Both PIKE-L and -A isoforms contain GTPase, pleckstrin homology (PH), ADP ribosylation factor-GTPase-activating protein, and two ankyrin repeats domains, and C-terminal ADP ribosylation factor-GTPase-activating protein activates its internal GTPase activity. However, whether PH domain modulates the intramolecular action and subsequently influences its downstream signalings remains elusive. Here we show that PH domain from PIKE-L robustly binds PI(3,4,5)P(3) and exclusively resides in the nucleus. By contrast, the mutant (K679,687N), unable to bind phosphoinositol lipids, translocates to the cytoplasm. This mutation substantially compromises the stimulatory effects on PI3-kinase by PIKE-L. Surprisingly, PH domain from PIKE-A distributes in the cytoplasm. Similar mutation in PH domain of PIKE-A abolishes its binding to PI(3,4,5)P(3) and significantly decreases its activation of Akt. Moreover, amplified PIKE-A from human cancers contains mutations and highly stimulates Akt kinase activity, correlating with its GTPase activity. Thus, phosphatidylinositols regulate PIKE GTPase activity, mediating its downstream PI3-kinase/Akt signaling through a feedback mechanism by binding to its PH domain.
BCl<sub>3</sub>-mediated polycoupling of alkynes and aldehydes: a facile, metal-free multicomponent polymerization route to construct stereoregular functional polymers (2016)

BCl<sub>3</sub>-mediated alkyne–aldehyde polymerization to stereoregular functional polymers in a facile, metal-free and multicomponent manner.
Label‐Free High‐Throughput Leukemia Detection by Holographic Microscopy (2018)

Complete blood count and differentiation of leukocytes (DIFF) belong to the most frequently performed laboratory diagnostic tests. Here, a flow cytometry-based method for label-free DIFF of untouched leukocytes by digital holographic microscopy on the rich phase contrast of peripheral leukocyte images, using highly controlled 2D hydrodynamic focusing conditions is reported. Principal component analysis of morphological characteristics of the reconstructed images allows classification of nine leukocyte types, in addition to different types of leukemia and demonstrates disappearance of acute myeloid leukemia cells in remission. To exclude confounding effects, the classification strategy is tested by the analysis of 20 blinded clinical samples. Here, 70% of the specimens are correctly classified with further 20% classifications close to a correct diagnosis. Taken together, the findings indicate a broad clinical applicability of the cytometry method for automated and reagent-free diagnosis of hematological disorders.
Effectiveness of ideal ratio mask for non-intrusive quality assessment of noise suppressed speech (2017)

The Ideal Ratio Mask (IRM) has proven to be very effective tool in many applications such as speech segregation, speech enhancement for hearing aid design and noise robust speech recognition tasks. The IRM provides information regarding the amount of signal power at each Time-Frequency (T-F) unit in a given signal-plus-noise mixture. In this paper, we propose to use the IRM for non-intrusive quality assessment of noise suppressed speech. Since the quality of noise suppressed speech is dependent on the residual noise present in speech, IRM can be extremely useful for its quality assessment. The quality assessment problem is posed as a regression problem and the mapping between statistics of acoustic features, namely, Mel Filterbank Energies (FBEs) plus IRM features and the subjective score of the corresponding utterances was found using single-layer Artificial Neural Network (ANN). The results of our experiments suggest that by using the mean of FBEs and IRM features as the input, the quality prediction accuracy was significantly increased.
Vaccinia E5 is a major inhibitor of the DNA sensor cGAS (2021)

SUMMARY The DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is largely unknown. In this study, we screened 82 vaccinia viral genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS that elicits proteasome-dependent cGAS degradation. E5 localizes to the cytoplasm and nuclei of infected cells. Cytosolic E5 triggers K48-linked ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. E5 itself also undergoes ubiquitination and degradation. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, thereby improving the immunogenicity of the viral vector.
Circadian rhythm of alpha-amylase in rat parotid gland. (1990)

The circadian rhythm of alpha-amylase, E.C. 3.2.1.1. (alpha-1,4-glucan-4-glucanohydrolase) in parotid gland of 25 day old rats was studied under different experimental conditions (fast, reversed photoperiod, constant light or darkness and treatment with reserpine and alpha-methyl-p-tyrosine). The rhythm of rats fasted or exposed for 7 days to constant darkness did not change. There were modifications in the rhythm of rats submitted to a reversed photoperiod and it disappeared in animals submitted to constant light or darkness for 15 days or treated with reserpine or alpha-methyl-p-tyrosine. The rhythm persisted, with minor changes in the acrophase, in parotids of rats kept during their gestation and post-natal life in constant light or darkness. Results suggest that the circadian rhythm of alpha-amylase in parotid gland of young rats is endogenous, synchronized by the photoperiod, under autonomous nervous system control and maternal coordination. This model appears to be useful in the study of sympathetic nervous system control of target organs and circadian rhythms in general.
Impaired glucose homeostasis in transgenic mice expressing the human transient neonatal diabetes mellitus locus, TNDM (2004)

Transient neonatal diabetes mellitus (TNDM) is a rare inherited diabetic syndrome apparent in the first weeks of life and again during early adulthood. The relative contributions of reduced islet β cell number and impaired β cell function to the observed hypoinsulinemia are unclear. The inheritance pattern of this imprinted disorder implicates overexpression of one or both genes within the TNDM locus: ZAC, which encodes a proapoptotic zinc finger protein, and HYMAI, which encodes an untranslated mRNA. To investigate the consequences for pancreatic function, we have developed a high-copy transgenic mouse line, TNDM29, carrying the human TNDM locus. TNDM29 neonates display hyperglycemia, and older adults, impaired glucose tolerance. Neonatal hyperglycemia occurs only on paternal transmission, analogous to paternal dependence of TNDM in humans. Embryonic pancreata of TNDM29 mice showed reductions in expression of endocrine differentiation factors and numbers of insulin-staining structures. By contrast, β cell mass was normal or elevated at all postnatal stages, whereas pancreatic insulin content in neonates and peak serum insulin levels after glucose infusion in adults were reduced. Expression of human ZAC and HYMAI in these transgenic mice thus recapitulates key features of TNDM and implicates impaired development of the endocrine pancreas and β cell function in disease pathogenesis.
A Hybrid Random Early Detection Algorithm for Improving End-to-End Congestion Control in TCP/IP Networks (2008)

The successful operation of the present Internet depends mainly upon TCP/IP which employs end-to-end congestion control mechanisms built in the end hosts. In order to further enhance this paradigm of end-to-end control the Random Early Detection algorithm (RED) has been proposed, which starts to mark or drop packets at the onset of congestion.  The paper addresses issues related to the choice of queue length  indication parameters for packet marking/dropping decisions  in RED-type algorithms under varying traffic conditions. Two modifications to RED are proposed: (i) use of both instantaneous queue size and its Exponential Weighted Moving Average (EWMA) for packet marking/dropping and (ii) reducing the effect of the EWMA queue size value when the queue size is less than  $min_{th}$ for a certain number of consecutive packet arrivals.   The newly developed Hybrid RED algorithm can effectively improve the performance of TCP/IP based networks while working in a control loop formed by either dropping or marking of packets during congestion epochs. New guidelines are developed for better marking/dropping of packets to achieve a faster response of RED-type algorithms. The hybrid RED algorithm has been tested using ns-2 simulations, which show better utilization of network bandwidth and a lower packet loss rate.
Model-based Force Estimation for Intra-cardiac Catheters (2015)

The objectives of this paper are twofold: first, presenting an efficient quasi-static model for intracardiac catheters, and second, proposing a real-time approach for the estimation of the force at the tip using the proposed model. The force estimation approach has the potential to be used in conjunction with previously developed pose sensing technologies to provide a sense of the forces applied by the catheter to the heart tissue in cardiac ablation procedures. The catheter is modeled as a planar elastica, consisting of consecutive circular curves. The parameters of the model are obtained through experiments, leading to a precise description of the shape of the catheter for the given external forces. The approach incorporates modeling of the compound system (distal shaft and catheter body) with inhomogeneous mechanical properties. The force estimation approach is based on the pose measurement of the catheter tip along with the identified parameters of the catheter model. As a result of the low dimensionality of the proposed quasi-static model, the inverse problem can be efficiently solved for the estimation of the external forces. The experiments performed using electromagnetic sensors verify the feasibility of the proposed scheme in medical applications.
Multiresolution 3-D range segmentation using focus cues (1998)

This paper describes a novel system for computing a three-dimensional (3-D) range segmentation of an arbitrary visible scene using focus information. The process of range segmentation is divided into three steps: an initial range classification, a surface merging process, and a 3-D multiresolution range segmentation. First, range classification is performed to obtain quantized range estimates. The range classification is performed by analyzing focus cues within a Bayesian estimation framework. A combined energy functional measures the degree of focus and the Gibbs distribution of the class field. The range classification provides an initial range segmentation. Second, a statistical merging process is performed to merge the initial surface segments. This gives a range segmentation at a coarse resolution. Third, 3-D multiresolution range segmentation (3-D MRS) is performed to refine the range segmentation into finer resolutions. The proposed range segmentation method does not require initial depth estimates, it allows the analysis of scenes containing multiple objects, and it provides a rich description of the 3-D structure of a scene.
Dose-volume histogram prediction using density estimation (2015)

Knowledge of what dose-volume histograms can be expected for a previously unseen patient could increase consistency and quality in radiotherapy treatment planning. We propose a machine learning method that uses previous treatment plans to predict such dose-volume histograms. The key to the approach is the framing of dose-volume histograms in a probabilistic setting.The training consists of estimating, from the patients in the training set, the joint probability distribution of some predictive features and the dose. The joint distribution immediately provides an estimate of the conditional probability of the dose given the values of the predictive features. The prediction consists of estimating, from the new patient, the distribution of the predictive features and marginalizing the conditional probability from the training over this. Integrating the resulting probability distribution for the dose yields an estimate of the dose-volume histogram.To illustrate how the proposed method relates to previously proposed methods, we use the signed distance to the target boundary as a single predictive feature. As a proof-of-concept, we predicted dose-volume histograms for the brainstems of 22 acoustic schwannoma patients treated with stereotactic radiosurgery, and for the lungs of 9 lung cancer patients treated with stereotactic body radiation therapy. Comparing with two previous attempts at dose-volume histogram prediction we find that, given the same input data, the predictions are similar.In summary, we propose a method for dose-volume histogram prediction that exploits the intrinsic probabilistic properties of dose-volume histograms. We argue that the proposed method makes up for some deficiencies in previously proposed methods, thereby potentially increasing ease of use, flexibility and ability to perform well with small amounts of training data.
Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1 (2021)

Pidilizumab is a monoclonal antibody tested against several types of malignancies, such as lymphoma and metastatic melanoma, showing promising results. In 2016, the FDA put Pidilizumab's clinical studies on partial hold due to emerging evidence pointing to the antibody target uncertainty. Although initial studies indicated an interaction with the PD-1 checkpoint receptor, recent updates assert that Pidilizumab binds primarily to Notch ligand DLL1. However, a detailed description of which interactions coordinate antibody-antigen complex formation is lacking. Therefore, this study uses computational tools to identify molecular interactions between Pidilizumab and its reported targets PD-1 and DLL1. A docking methodology was validated and applied to determine the binding modes between modeled Pidilizumab scFvs and the two antigens. We used Molecular Dynamics (MD) simulations to verify the complexes' stability and submitted the resulting trajectory files to MM/PBSA and Principal Component Analysis. A set of different prediction tools determined scFv interface hot-spots. Whereas docking and MD simulations revealed that the antibody fragments do not interact straightforwardly with PD-1, ten scFv hot-spots, including Met93 and Leu112, mediated the interaction with the DLL1 C2 domain. The interaction triggered a conformational selection-like effect on DLL1, allowing new hydrogen bonds on the β3-β4 interface loop. The unprecedented structural data on Pidilizumab's interactions provided novel evidence that its legitimate target is the DLL1 protein and offered structural insight on how these molecules interact, shedding light on the pathways that could be affected by the use of this essential immunobiological. Communicated by Ramaswamy H. Sarma.