gebhart/patrepeval huggingface dataset:
Comparative Analysis of Entity Identification and Classification of Indian Epics (2022)

Despite the relevance and accessibility of Indian epics such as the Mahabharata, little research has been done on the corpus in Natural Language Processing (NLP). To revitalize NLP research on the Indian epics, we present a computational analysis of SOTA supervised Machine Learning (ML) methods for Named Entity Recognition (NER) using our annotated dataset of labeled tokens of the Mahabharata text. The text contains English and Sanskrit words, offering a different vocabulary than modern literature. The characters also change their nature throughout the storyline, challenging many SOTA NER methods as tokens with the same name can have different entity types. For example, we discover that NLTK inaccurately identifies 95% tokens as named entities. We also note that spaCy and Stanford NER perform adequately only after training. However, since they produce one embedding per token, they fail to distinguish between entities with the same name. In contrast, context-driven methods such as BERT and ELMO tackle the issue as they produce different embeddings. Yet, ELMO delivers poor results due to its character-based embeddings and pseudo-bidirectionality. BERT performs the best with a 0.98 micro-avg F1 score but overfits the dataset. Therefore, the current SOTA techniques are unsuitable for NER on the Indian epics, and more research is needed to build a universally suited NER agent capable of recognizing named entities from diverse cultural contexts.
Two-dimensional encoding by finite-state encoders (1990)

Distortion-free compressibility of individual pictures by finite-state encoders is investigated. In a recent paper (see IEEE Trans. Inform. Theory, vol.32, no.1, p.1-8, 1986) the compressibility of a given picture I was defined and shown to be the asymptotically attainable lower bound on the compression ratio that can be achieved for I by any finite-state encoder. Here, a different and more direct approach is taken to prove similar results, which are summarized in a converse-to-coding theorem and a constructive-coding-theorem that leads to a universal asymptotically optimal compression algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Assessment of MALDI-TOF MS as Alternative Tool for Streptococcus suis Identification (2015)

The accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identifying Streptococcus suis isolates obtained from pigs, wild animals, and humans was evaluated using a PCR-based identification assay as the gold standard. In addition, MALDI-TOF MS was compared with the commercial multi-tests Rapid ID 32 STREP system. From the 129 S. suis isolates included in the study and identified by the molecular method, only 31 isolates (24.03%) had score values ≥2.300 and 79 isolates (61.24%) gave score values between 2.299 and 2.000. After updating the currently available S. suis MALDI Biotyper database with the spectra of three additional clinical isolates of serotypes 2, 7, and 9, most isolates had statistically significant higher score values (mean score: 2.65) than those obtained using the original database (mean score: 2.182). Considering the results of the present study, we suggest using a less restrictive threshold score of ≥2.000 for reliable species identification of S. suis. According to this cut-off value, a total of 125 S. suis isolates (96.9%) were correctly identified using the updated database. These data indicate an excellent performance of MALDI-TOF MS for the identification of S. suis.
Supplementary Figure 1 from Suppression of Prostate Cancer Nodal and Systemic Metastasis by Blockade of the Lymphangiogenic Axis (2023)

Supplementary Figure 1 from Suppression of Prostate Cancer Nodal and Systemic Metastasis by Blockade of the Lymphangiogenic Axis
New Nanocrystalline Cu/MnOx Catalysts Prepared from Supercritical Antisolvent Precipitation (2009)

Abstract Supercritical CO 2 is used as an antisolvent to precipitate out nanostructured homogeneous mixtures of Cu 2+ and Mn 3+ with crystallites of 10–20 nm in diameter. Following calcination, this material forms a crystalline tetragonal spinel, CuMn 2 O 4 , with a branched chainlike structure with a length of 160–200 nm and diameters of approximately 40 nm. This new material is more than twice as active per unit surface area as the conventionally prepared hopcalite catalysts for the oxidation of carbon monoxide. This is the first time that homogeneous mixed oxides have been formed using this method.
Rational Management of Charge Transfer Character of Benzothienopyrimidine‐Based N‐Type Host for Blue Phosphorescent Organic Light‐Emitting Diodes (2021)

Abstract Two materials, 3‐(4‐(9H‐carbazol‐9‐yl)benzo[4,5]thieno[3,2‐d]pyrimidin‐2‐yl)‐5‐(triphenylsilyl)benzonitrile (CzBTPCNmSi) and 9‐(2‐(3‐(triphenylsilyl)phenyl)benzo[4,5]thieno[3,2‐d]pyrimidin‐4‐yl)‐9H‐carbazole‐3‐carbonitrile (CNCzBTPmSi), are synthesized as the N‐type host (electron‐transport type host) of a mixed host, harvesting triplet excitons of the blue phosphor by engineering the charge transfer character using a CN unit. The two host materials are based on benzothienopyrmidine modified using CN, tetraphenylsilyl, and carbazole groups to control the lowest unoccupied molecular orbital level, manage their intermolecular packing, and stabilize the molecule against holes, respectively. The two hosts are mixed with a P‐type 3,3‐di(9H‐carbazol‐9‐yl)biphenyl (mCBP) to offer a mixed host for sky and deep blue‐emitting phosphors. In the device applications, CzBTPCNmSi and CNCzBTPmSi show high external quantum efficiency (EQE) (around 24% in the sky‐blue devices), whereas only CNCzBTPmSi exhibited high EQE (above 20% in the deep blue devices) due to high triplet energy. Moreover, the CNCzBTPmSi demonstrates a longer device lifetime than the control host without the CN unit. Thus, CN engineering can manage the triplet energy, EQE, and device lifetime of blue phosphorescent devices by controlling the charge transfer character.
Constellation randomization (CoRa) for outage performance improvement on MIMO channels (2005)

This work studies a new concept, "constellation randomization" (CoRa), for performance improvement of transmission over quasi-static (block fading) multidimensional ("MIMO") channels with small signal constellations. The motivation behind CoRa is to reduce some of the mutual information penalty associated with the use of a finite input alphabet for signalling on a static, possibly ill-conditioned, channel. We show, both via information-theoretic considerations, and via Monte-Carlo simulation of the frame-error-rate (FER) of a coded system, that CoRa can offer a lower outage probability than a conventional spatial multiplexing system that uses a fixed signal constellation. In our examples the improvement offered by CoRa is comparable to that offered by linear (complex-field) precoding. This is interesting, because the performance gain of CoRa comes at virtually no computational expense.
Inclusion of the Bovine Neutrophil Beta-Defensin 3 with Glycoprotein D of Bovine Herpesvirus 1 in a DNA Vaccine Modulates Immune Responses of Mice and Cattle (2014)

Bovine herpesvirus 1 (BoHV-1) causes recurrent respiratory and genital infections in cattle and predisposes them to lethal secondary infections. While modified live and killed BoHV-1 vaccines exist, these are not without problems. Development of an effective DNA vaccine for BoHV-1 has the potential to address these issues. As a strategy to enhance DNA vaccine immunity, a plasmid encoding the bovine neutrophil beta-defensin 3 (BNBD3) as a fusion with truncated glycoprotein D (tgD) and a mix of two plasmids encoding BNBD3 and tgD were tested in mice and cattle. In mice, coadministration of BNBD3 on the separate plasmid enhanced the tgD-induced gamma interferon (IFN-γ) response but not the antibody response. BNBD3 fused to tgD did not affect the antibody levels or the number of IFN-γ-secreting cells but increased the induction of tgD-specific cytotoxic T lymphocytes (CTLs). In cattle, the addition of BNBD3 as a fusion construct also modified the immune response. While the IgG and virus-neutralizing antibody levels were not affected, the number of IFN-γ-secreting cells was increased after BoHV-1 challenge, specifically the CD8(+) IFN-γ(+) T cells, including CD8(+) IFN-γ(+) CD25(+) CTLs. While reduced virus shedding, rectal temperature, and weight loss were observed, the level of protection was comparable to that observed in pMASIA-tgD-vaccinated animals. These data show that coadministration of BNBD3 with a protective antigen as a fusion in a DNA vaccine strengthened the Th1 bias and increased cell-mediated immune responses but did not enhance protection from BoHV-1 infection.
Biomimetic Periodontal Ligament Transplantation Activated by Gold Nanoparticles Protects Alveolar Bone (2023)

Stem cell therapy might be a promising method to stimulate alveolar bone regeneration, which is currently a major clinical challenge. However, its therapeutic features largely depend on pretreatment and transplantation preparation. Herein, a novel biomimetic periodontal ligament transplantation composed of human periodontal ligament stem cells (hPDLSCs) pretreated with gold nanocomplexes (AuNCs) and embedded in a type-I collagen hydrogel scaffold is developed to protect alveolar bone from resorption. AuNCs are readily absorbed by primary hPDLSCs, with limited cytotoxicity, and promote osteogenic differentiation of hPDLSCs effectively in vitro. In addition, the AuNCs-induced hPDLSCs are encapsulated with type-I collagen hydrogel scaffold to mimic their native physiological niche, and then are transplanted into a rat model of alveolar bone resorption. Both micro-computed tomography (micro-CT) and immunohistochemical assays demonstrate that alveolar bone loss is significantly prevented. Furthermore, the underlying therapeutic mechanism is elucidated, in which transplantation-activated osteogenesis is associated with autophagy, which enables bone remodeling and regeneration. This study provides critical insight into the role of PDLSCs in bone homeostasis and proposes an innovative AuNCs-based strategy for stem cell therapy in bone regeneration.
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): Where will the drugs come from? (2021)

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic debilitating disease characterized by severe and disabling fatigue that fails to improve with rest; it is commonly accompanied by multifocal pain, as well as sleep disruption, and cognitive dysfunction. Even mild exertion can exacerbate symptoms. The prevalence of ME/CFS in the U.S. is estimated to be 0.5-1.5 % and is higher among females. Viral infection is an established trigger for the onset of ME/CFS symptoms, raising the possibility of an increase in ME/CFS prevalence resulting from the ongoing COVID-19 pandemic. Current treatments are largely palliative and limited to alleviating symptoms and addressing the psychological sequelae associated with long-term disability. While ME/CFS is characterized by broad heterogeneity, common features include immune dysregulation and mitochondrial dysfunction. However, the underlying mechanistic basis of the disease remains poorly understood. Herein, we review the current understanding, diagnosis and treatment of ME/CFS and summarize past clinical studies aimed at identifying effective therapies. We describe the current status of mechanistic studies, including the identification of multiple targets for potential pharmacological intervention, and ongoing efforts towards the discovery of new medicines for ME/CFS treatment.
SupplementaryMethods.docx from Oncostatin M Receptor–Targeted Antibodies Suppress STAT3 Signaling and Inhibit Ovarian Cancer Growth (2023)

SupplementaryMethods.docx from Oncostatin M Receptor–Targeted Antibodies Suppress STAT3 Signaling and Inhibit Ovarian Cancer Growth
Syntheses of new ruthenium clusters containing sulfur, ynyl and diynyl ligands. Crystal structures of [Ru3(CO)9(µ-η2-SCCSiMe3)(µ3-η2-CCSiMe3)], [Ru4(CO)12(µ4-S)(µ-η2-CCSiMe3)2] and [Ru4(CO)9(µ-CO)2(µ4-S)(µ4-η2-C(SiMe3)C(CCSiMe3)] (2001)

Reaction of Ru3(CO)12 and S(CCSiMe3)2 in toluene gave [Ru3(CO)9(μ-η2-SCCSiMe3)(μ3-η2-CCSiMe3)] 1. The thermolysis of 1 provokes the rupture of the S–Csp bond of the SCCSiMe3 ligand and C–C coupling reactions between two acetylide groups affording the clusters [Ru3(CO)9(μ3-S)(μ3-η2-C(SiMe3)C(CCSiMe3)] 2, [Ru2(CO)6(μ-η3-SCCSiMe3)(μ-η2-CCSiMe3)] 3, [Ru4(CO)12(μ4-S)(μ-η2-CCSiMe3)2] 4 and [Ru4(CO)9(μ-CO)2(μ4-S)(μ4-η2-C(SiMe3)C(CCSiMe3)] 5. All compounds have been characterized by IR and NMR techniques as well as FAB+ mass spectrometry. Crystal structures of 1, 4, and 5 have been determined by X-ray diffraction methods. The pathways of the thermolysis of 1 to give 2–5 have been investigated.
Effects of Diarylheptanoids on the Tumor Necrosis Factor-α-Induced Expression of Adhesion Molecules in Human Umbilical Vein Endothelial Cells (2007)

Atherosclerosis is a chronic inflammatory disease that is characterized by infiltration of mononuclear lymphocytes into the intima through the expression of adhesion molecules on the arterial wall. In the present study, we report the inhibitory effects of two diarylheptanoids, 5-O-methylhirsutanonol (1) and oregonin (2), isolated from the methanolic extracts of Alnus japonica leaves, on the expression of adhesion molecules in human umbilical vein endothelial cells (HUVECs). Compounds 1 and 2 inhibited tumor necrosis factor (TNF)-alpha-induced up-regulation of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1), which also prevented adhesion of monocytes to HUVECs, and slightly suppressed the mRNA expression of the inflammation-associated gene interleukin-1beta (IL-1beta). A further study demonstrated the inhibitory effect of compound 1 on DNA-binding of nuclear factor kappaB (NF-kappaB) and on the phosphorylation and degradation of inhibitory factor kappaBalpha (IkappaBalpha) in TNF-alpha-stimulated HUVECs. These results indicate that compounds 1 and 2 may be useful in the prevention and treatment of atherosclerosis through attenuation of adhesion molecule expression by inhibition of NF-kappaB activation.
Homologous-pairing activity of the human DNA-repair proteins Xrcc3⋅Rad51C (2001)

The human Xrcc3 protein is involved in the repair of damaged DNA through homologous recombination, in which homologous pairing is a key step. The Rad51 protein is believed to be the only protein factor that promotes homologous pairing in recombinational DNA repair in mitotic cells. In the brain, however, Rad51 expression is extremely low, whereas XRCC3, a human homologue of Saccharomyces cerevisiae RAD57 that activates the Rad51-dependent homologous pairing with the yeast Rad55 protein, is expressed. In this study, a two-hybrid analysis conducted with the use of a human brain cDNA library revealed that the major Xrcc3-interacting protein is a Rad51 paralog, Rad51C/Rad51L2. The purified Xrcc3.Rad51C complex, which shows apparent 1:1 stoichiometry, was found to catalyze the homologous pairing. Although the activity is reduced, the Rad51C protein alone also catalyzed homologous pairing, suggesting that Rad51C is a catalytic subunit for homologous pairing. The DNA-binding activity of Xrcc3.Rad51C was drastically decreased in the absence of Xrcc3, indicating that Xrcc3 is important for the DNA binding of Xrcc3.Rad51C. Electron microscopic observations revealed that Xrcc3.Rad51C and Rad51C formed similar filamentous structures with circular single-stranded DNA.
Lack of durable protection against cotton smoke‐induced acute lung injury in sheep by nebulized single chain urokinase plasminogen activator or tissue plasminogen activator (2018)

Physiologic outcomes improved in sheep in which better delivery of the PAs occurred. The benefits of nebulized scuPA were achieved without airway bleeding associated with tPA, but were transient and largely abrogated at 48 h, in part attributable to the progression and severity of ISIALI.
Assessing therapeutic effectiveness of scalp treatments for dandruff and seborrheic dermatitis, part 1: a reliable and relevant method based on the adherent scalp flaking score (ASFS) (2012)

The ASFS-based clinical model was demonstrated to be a reliable and proven methodology to assess the effectiveness of widely used anti-dandruff treatments. The results are consistent with patient self-assessments, establishing this methodology as relevant to patient perception of product benefits.
Adiponectin deficiency: a model of pulmonary hypertension associated with pulmonary vascular disease (2009)

Adiponectin (APN) is an adipocyte-derived factor that exists at high concentrations in serum and has anti-inflammatory and systemic vascular-protective properties. In this study, we investigated the role of APN in pulmonary vascular homeostasis. We found that APN localizes to the luminal side of blood vessels in lung and acts in vitro to block TNF-alpha-induced E-selectin upregulation in pulmonary artery endothelial cells. Targeted deletion of the APN gene in mice leads to a vascular phenotype in lung characterized by E-selectin upregulation and age-dependent increases in perivascular inflammatory cell infiltration and pulmonary arterial pressures. Taken together, these findings demonstrate an important role for APN in lung vascular homeostasis and suggest that APN-deficient states may contribute to the pathogenesis of inflammatory pulmonary vascular disease and to the development of pulmonary hypertension.
Stem Cell Transplant into Preimplantation Embryo Yields Myocardial Infarction-Resistant Adult Phenotype (2009)

Stem cells are an emerging strategy for treatment of myocardial infarction, limited however to postinjury intervention. Preventive stem cell-based therapy to augment stress tolerance has yet to be considered for lifelong protection. Here, pluripotent stem cells were microsurgically introduced at the blastocyst stage of murine embryo development to ensure stochastic integration and sustained organ contribution. Engineered chimera displayed excess in body weight due to increased fat deposits, but were otherwise devoid of obesity-related morbidity. Remarkably, and in sharp contrast to susceptible nonchimeric offspring, chimera was resistant to myocardial infarction induced by permanent coronary occlusion. Infarcted nonchimeric adult hearts demonstrated progressive deterioration in ejection fraction, while age-matched 12-14-months-old chimera recovered from equivalent ischemic insult to regain within one-month preocclusion contractile performance. Electrical remodeling and ventricular enlargement with fibrosis, prominent in failing nonchimera, were averted in the chimeric cohort characterized by an increased stem cell load in adipose tissue and upregulated markers of biogenesis Ki67, c-Kit, and stem cell antigen-1 in the myocardium. Favorable outcome in infarcted chimera translated into an overall benefit in workload capacity and survival. Thus, prenatal stem cell transplant yields a cardioprotective phenotype in adulthood, expanding cell-based indications beyond traditional postinjury applications to include pre-emptive therapy.
Recovery of Fuel-Precursor Lipids from Oleaginous Yeast (2018)

Bioderived lipids offer a potentially promising intermediate to displace petroleum-derived diesel. One of the key challenges for the production of lipids via microbial cell mass is that these products are stored intracellularly and must be extracted and recovered efficiently and economically. Thus, improved methods of cell lysis and lipid extraction are needed. In this study, we examine lipid extraction from wet oleaginous yeast in combination with seven different cell lysis approaches encompassing both physical and chemical techniques (high-pressure homogenization, microwave and conventional thermal treatments, bead beating, acid, base, and enzymatic treatments) to facilitate lipid extraction from a model oleaginous yeast strain, Lipomyces starkeyi. Of the seven techniques investigated, acid treatment led to the highest lipid recovery yields. Further exploration of acid treatment and integration with an economic model revealed that treatment at 170 °C for 60 min at 1 wt % H2SO4 and 8 wt % yeast solids represents a viable option for both lipid recovery yield and process economics, enabling experimental lipid recovery yields of 88.5–93.0% to be achieved at a corresponding estimated minimum fuel selling price (MFSP) of $5.13–$5.61/gallon of gasoline equivalent (GGE). The same acid treatment conditions applied to two other strains of oleaginous yeast (Cutaneotrichosporon curvatus and Rhodotorula toruloides) resulted in similar lipid recovery yields. In pretreatment experiments scaled up to 300 mL, slightly lower temperatures or shorter pretreatment times, along with higher yeast solids loading, resulted in higher lipid yields than the conditions identified from the small-scale runs. Two replicate runs carried out at 170 °C for 30 min using 1 wt % H2SO4 and 19 wt % yeast solids achieved an average lipid recovery of 96.1% at a corresponding estimated MFSP of $4.89/GGE. In all cases, the lipids are primarily triglycerides and free fatty acids comprised mainly of palmitic, stearic, and oleic acids, with smaller fractions of polar lipids. The fatty acid composition of the lipids extracted from the wet treated cell mass is the same as that in freeze-dried whole oleaginous yeast cell mass, suggesting the acid treatment renders all lipids extractable. This work demonstrates that acid treatment is a robust and effective cell lysis technique in a microbial lipid-based biofuel scenario and provides a baseline for further scale-up and process integration.
Sparse Topical Coding (2012)

We present sparse topical coding (STC), a non-probabilistic formulation of topic models for discovering latent representations of large collections of data. Unlike probabilistic topic models, STC relaxes the normalization constraint of admixture proportions and the constraint of defining a normalized likelihood function. Such relaxations make STC amenable to: 1) directly control the sparsity of inferred representations by using sparsity-inducing regularizers; 2) be seamlessly integrated with a convex error function (e.g., SVM hinge loss) for supervised learning; and 3) be efficiently learned with a simply structured coordinate descent algorithm. Our results demonstrate the advantages of STC and supervised MedSTC on identifying topical meanings of words and improving classification accuracy and time efficiency.