gebhart/patrepeval huggingface dataset:
Aerobic H2 production related to formate metabolism in white-rot fungi (2023)

Biohydrogen is mainly produced by anaerobic bacteria, anaerobic fungi, and algae under anaerobic conditions. In higher eukaryotes, it is thought that molecular hydrogen (H<sub>2</sub>) functions as a signaling molecule for physiological processes such as stress responses. Here, it is demonstrated that white-rot fungi produce H<sub>2</sub> during wood decay. The white-rot fungus <i>Trametes versicolor</i> produces H<sub>2</sub> from wood under aerobic conditions, and H<sub>2</sub> production is completely suppressed under hypoxic conditions. Additionally, oxalate and formate supplementation of the wood culture increased the level of H<sub>2</sub> evolution. RNA-seq analyses revealed that <i>T. versicolor</i> oxalate production from the TCA/glyoxylate cycle was down-regulated, and conversely, genes encoding oxalate and formate metabolism enzymes were up-regulated. Although the involvement in H<sub>2</sub> production of a gene annotated as an iron hydrogenase was uncertain, the results of organic acid supplementation, gene expression, and self-recombination experiments strongly suggest that formate metabolism plays a role in the mechanism of H<sub>2</sub> production by this fungus. It is expected that this novel finding of aerobic H<sub>2</sub> production from wood biomass by a white-rot fungus will open new fields in biohydrogen research.
RISK FACTORS FOR DIABETES IN THREE PACIFIC POPULATIONS (1984)

The association between the prevalence of diabetes and three suspected risk factors--overweight, physical inactivity, and urbanization--has been studied in 5519 subjects from three Pacific populations: Melanesians and migrant Asian Indians in Fiji in 1980, and Micronesians in the Republic of Kiribati (formerly the Gilbert Islands) in 1981. Associations were found to be inconsistent between populations, and between the sexes within populations. In some cases, overweight was strongly associated with prevalence; in others, the principal variable associated with diabetes appeared to be physical inactivity. More than one factor was associated with increased risk in Micronesians, and some evidence of interaction between factors also emerged. Although longitudinal studies will be required for the complete elucidation of risk factors for diabetes, these findings suggest that risk factors may be heterogeneous in their effect upon different populations, and that an assessment of risk variables operating in a given target community may be of value in the initial phase of a diabetes prevention or control program.
InGaAs quantum dot lasers with sub-milliamp thresholdsand ultra-low threshold current density below room temperature (2000)

Continuous-wave operation of InGaAs quantum dot lasers is studied. A very low threshold current of 460 µA is achieved at 200 K for a 5 µm × 1170 µm oxide-confined stripe laser. For a larger stripe width of 11 µm, a threshold current density of 5.2 A/cm2 is demonstrated. The characteristic threshold temperature is ~700 K in the temperature range of 140–200 K, and drops rapidly around room temperature.
Supplementary Figure S2 from Integrative Analysis of DCE-MRI and Gene Expression Profiles in Construction of a Gene Classifier for Assessment of Hypoxia-Related Risk of Chemoradiotherapy Failure in Cervical Cancer (2023)

&lt;p&gt;Comparing Illumina and RT-qPCR gene expression data.&lt;/p&gt;
Dynamic Clustering for GNSS Positioning with Multiple Receivers (2022)

We consider the problem of jointly estimating the states of multiple global navigation satellite system (GNSS) receivers modeled with shared biases. In particular, we explore how to best assign these receivers to disjoint sets, so as to retain computational feasibility in the resulting filters. We propose a genetic algorithm that dynamically assigns agents to clusters subject to constraints on the maximum number of states in the clusters. Several numerical examples illustrate the flexibility of the approach, and the choice of genetic operations in the clustering algorithm is motivated by their effect on the algorithm's expected convergence rate. Numerical experiments with a GNSS-inspired problem demonstrates that the proposed clustering can yield a substantial improvements in the mean-square error compared to a random cluster assignment.
Data from Clinical Importance of the lncRNA <i>NEAT1</i> in Cancer Patients Treated with Immune Checkpoint Inhibitors (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;mAbs targeting the PD-1/PD-L1 immune checkpoint are powerful tools to improve the survival of patients with cancer. Understanding the molecular basis of clinical response to these treatments is critical to identify patients who can benefit from this immunotherapy. In this study, we investigated long noncoding RNA (lncRNA) expression in patients with cancer treated with anti-PD-1/PD-L1 immunotherapy.&lt;/p&gt;Experimental Design:&lt;p&gt;lncRNA expression profile was analyzed in one cohort of patients with melanoma and two independent cohorts of patients with glioblastoma (GBM) undergoing anti-PD-1/PD-L1 immunotherapy. Single-cell RNA-sequencing analyses were performed to evaluate lncRNA expression in tumor cells and tumor-infiltrating immune cells.&lt;/p&gt;Results:&lt;p&gt;We identified the lncRNA &lt;i&gt;NEAT1&lt;/i&gt; as commonly upregulated between patients with melanoma with complete therapeutic response and patients with GBM with longer survival following anti-PD-1/PD-L1 treatment. Gene set enrichment analyses revealed that &lt;i&gt;NEAT1&lt;/i&gt; expression was strongly associated with the IFNγ pathways, along with downregulation of cell-cycle-related genes. Single-cell RNA-sequencing analyses revealed &lt;i&gt;NEAT1&lt;/i&gt; expression across multiple cell types within the GBM microenvironment, including tumor cells, macrophages, and T cells. High &lt;i&gt;NEAT1&lt;/i&gt; expression levels in tumor cells correlated with increased infiltrating macrophages and microglia. In these tumor-infiltrating myeloid cells, we found that &lt;i&gt;NEAT1&lt;/i&gt; expression was linked to enrichment in TNFα/NFκB signaling pathway genes. Silencing &lt;i&gt;NEAT1&lt;/i&gt; suppressed M1 macrophage polarization and reduced the expression of TNFα and other inflammatory cytokines.&lt;/p&gt;Conclusions:&lt;p&gt;These findings suggest an association between &lt;i&gt;NEAT1&lt;/i&gt; expression and patient response to anti-PD-1/PD-L1 therapy in melanoma and GBM and have important implications for the role of lncRNAs in the tumor microenvironment.&lt;/p&gt;&lt;/div&gt;
High‐resolution separation of PCR product and gene diagnosis by capillary gel electrophoresis (1994)

High-resolution separation of a PCR product from a mixture of DNA restriction fragments was achieved using capillary gel electrophoresis. The capillary gel electrophoretic separation gives an excellent resolution of two fragments of the 500-bp PCR product and the 506-bp DNA fragment, which differs by only 6 bp, and the complete separation of a broader chain length range of DNA afragments up to 12 kbp within 20 min. The plate number of gel-filled capillary was achieved to be 2 million plates per meter. Capillary gel electrophoresis is applied to the gene diagnosis for heart disease through apolipoprotein E genotyping. The advantages and limitations of capillary gel electrophoresis in the application to PCR analysis and DNA diagnosis are discussed.
High-Density Electrical Recording and Impedance Imaging With a Multi-Modal CMOS Multi-Electrode Array Chip (2019)

Multi-electrode arrays, both active or passive, emerged as ideal technologies to unveil intricated electrophysiological dynamics of cells and tissues. Active MEAs, designed using complementary metal oxide semiconductor technology (CMOS), stand over passive devices thanks to the possibility of achieving single-cell resolution, the reduced electrode size, the reduced crosstalk and the higher functionality and portability. Nevertheless, most of the reported CMOS MEA systems mainly rely on a single operational modality, which strongly hampers the applicability range of a single device. This can be a limiting factor considering that most biological and electrophysiological dynamics are often based on the synergy of multiple and complex mechanisms acting from different angles on the same phenomena. Here, we designed a CMOS MEA chip with 16,384 titanium nitride electrodes, 6 independent operational modalities and 1,024 parallel recording channels for neuro-electrophysiological studies. Sixteen independent active areas are patterned on the chip surface forming a 4 × 4 matrix, each one including 1,024 electrodes. Electrodes of four different sizes are present on the chip surface, ranging from 2.5 × 3.5 μm<sup>2</sup> up to 11 × 11.0 μm<sup>2</sup>, with 15 μm pitch. In this paper, we exploited the impedance monitoring and voltage recording modalities not only to monitor the growth and development of primary rat hippocampal neurons, but also to assess their electrophysiological activity over time showing a mean spike amplitude of 144.8 ± 84.6 μV. Fixed frequency (1 kHz) and high sampling rate (30 kHz) impedance measurements were used to evaluate the cellular adhesion and growth on the chip surface. Thanks to the high-density configuration of the electrodes, as well as their dimension and pitch, the chip can appreciate the evolutions of the cell culture morphology starting from the moment of the seeding up to mature culture conditions. The measurements were confirmed by fluorescent staining. The effect of the different electrode sizes on the spike amplitudes and noise were also discussed. The multi-modality of the presented CMOS MEA allows for the simultaneous assessment of different physiological properties of the cultured neurons. Therefore, it can pave the way both to answer complex fundamental neuroscience questions as well as to aid the current drug-development paradigm.
Lithium Diffusion in Li4/3Ti5/3O4 Particles during Insertion and Extraction (2011)

Lithium diffusion in a small Li 4/3 Ti 5/3 O 4 (LTO) particle was investigated from kinetic viewpoints of two-phase transition process based on a core-shell model by means of galvanostatic and potentiostatic measurements of thin LTO composite electrodes. High-rate galvanostatic charge (insertion) – discharge (extraction) properties of the thin LTO composite electrode showed that the insertion into the LTO particle was significantly slower than the extraction. An apparent chemical diffusion coefficient ( D app ) of lithium in the LTO particle during the insertion and extraction was evaluated from the results of potential step chronoamperometry (PSCA) with a spherical finite diffusion model. The phase-boundary movements between the two phases in the cathodic and the anodic potential steps for a long-time region were controlled by lithium diffusion through Li 7/3 Ti 5/3 O 4 rock-salt (LTO-rock-salt) and Li 4/3 Ti 5/3 O 4 spinel (LTO-spinel) shell, respectively. D app in the LTO-rock-salt and the LTO-spinel phase were estimated to be approximately 1 × 10 −12 cm 2 /s and 1.6 × 10 −11 cm 2 /s, respectively. The slower insertion was mainly due to a D app value one order of magnitude smaller in the LTO-rock-salt than that in the LTO-spinel phase. Electrochemical kinetic properties of the LTO particle with the core-shell structure were interpreted by lithium diffusion through the LTO-rock-salt shell during the insertion and the LTO-spinel shell with the low electron conductivity during the extraction.
Laser-induced darkening in semiconductor-doped glasses (1991)

We have performed experiments to characterize permanent laser-induced darkening in CdSxSe1−x semiconductor-doped glasses with picosecond pulses as a function of fluence, repetition rate, and pulse width. We find that the darkening occurs by means of a nonlinear process that exhibits an anomalous dependence on pulse width. Transmission spectra show that the induced darkening is uniform over the spectral range from the absorption edge out to 820 μm. Darkening in a number of different glasses is compared. On the basis of our results we propose a mechanism that involves photoassisted trapping of electrons from the semiconductor microcrystallites into states within the glass host material.
Cancer cachexia-induced muscle atrophy: evidence for alterations in microRNAs important for muscle size (2017)

Muscle atrophy is a hallmark of cancer cachexia resulting in impaired function and quality of life and cachexia is the immediate cause of death for 20-40% of cancer patients. Multiple microRNAs (miRNAs) have been identified as being involved in muscle development and atrophy; however, less is known specifically on miRNAs in cancer cachexia. The purpose of this investigation was to examine the miRNA profile of skeletal muscle atrophy induced by cancer cachexia to uncover potential miRNAs involved with this catabolic condition. Phosphate-buffered saline (PBS) or Lewis lung carcinoma cells (LLC) were injected into C57BL/6J mice at 8 wk of age. LLC animals were allowed to develop tumors for 4 wk to induce cachexia. Tibialis anterior muscles were extracted and processed to isolate small RNAs, which were used for miRNA sequencing. Sequencing results were assembled with mature miRNAs, and functions of miRNAs were analyzed by Ingenuity Pathway Analysis. LLC animals developed tumors that contributed to significantly smaller tibialis anterior muscles (18.5%) and muscle cross-sectional area (40%) compared with PBS. We found 371 miRNAs to be present in the muscle above background levels. Of these, nine miRNAs were found to be differentially expressed. Significantly altered groups of miRNAs were categorized into primary functionalities including cancer, cell-to-cell signaling, and cellular development among others. Gene network analysis predicted specific alterations of factors contributing to muscle size including Akt, FOXO3, and others. These results create a foundation for future research into the sufficiency of targeting these genes to attenuate muscle loss in cancer cachexia.
Impedance Measurement of a Dipole Above a Periodically Structured Reflective Surface (2008)

The impedance of a horizontal dipole antenna placed closely above a periodically structured reflective surface was determined. In order to characterize the antenna directly at its feed point, a measurement technique is suggested where the influence of the feed network is eliminated. Implications of the reflective surface on the dipole impedance are discussed in detail. Furthermore, the radiation pattern and the total efficiency of a low-profile dipole are investigated quantitatively.
Heat Flow Measurement by Force and Thermal Sensor Stick with Nerve-net LSI Chip (2019)

Assistant robots need a tactile sensing system. We propose a tactile sensor head with a nerve-net sensing system which measures force, temperature and heat flow on robot fingers. For accurate heat flow measurements, it is necessary to stabilize contact conditions between the sensor head and objects. A sensor stick which consists of the sensor head and an actuator was fabricated to control applied force. Heat flow measurements in three materials of different thermal conductivities such as polyethylene, glass and aluminum were examined with the sensor stick. For the measurement, the sensor head was heated at 0.55W and brought into contact with the measurement object for 180s. Materials were discriminated clearly by temperature changes and heat flow changes. Finally, 13 kinds of materials with different thermal conductivities were measured. Under 10W/mK in thermal conductivities of measurement objects, heat flow peaks, heat flow saturations and heat flow time constants showed good correlations with the thermal conductivities. Over 10W/mK heat flow peaks, heat flow saturations and heat flow time constants were saturated to 0.7W, 0.4W and 40s, respectively. The tactile sensor stick with heat flow measurement and force control is useful to discriminate materials of objects as smart as a human being.
The folding landscape of an α‐lytic protease variant reveals the role of a conserved β‐hairpin in the development of kinetic stability (2005)

Most secreted bacterial proteases, including alpha-lytic protease (alphaLP), are synthesized with covalently attached pro regions necessary for their folding. The alphaLP folding landscape revealed that its pro region, a potent folding catalyst, is required to circumvent an extremely large folding free energy of activation that appears to be a consequence of its unique unfolding transition. Remarkably, the alphaLP native state is thermodynamically unstable; a large unfolding free energy barrier is solely responsible for the persistence of its native state. Although alphaLP folding is well characterized, the structural origins of its remarkable folding mechanism remain unclear. A conserved beta-hairpin in the C-terminal domain was identified as a structural element whose formation and positioning may contribute to the large folding free energy barrier. In this article, we characterize the folding of an alphaLP variant with a more favorable beta-hairpin turn conformation (alphaLP(beta-turn)). Indeed, alphaLP(beta-turn) pro region-catalyzed folding is faster than that for alphaLP. However, instead of accelerating spontaneous folding, alphaLP(beta-turn) actually unfolds more slowly than alphaLP. Our data support a model where the beta-hairpin is formed early, but its packing with a loop in the N-terminal domain happens late in the folding reaction. This tight packing at the domain interface enhances the kinetic stability of alphaLP(beta-turn), to nearly the same degree as the change between alphaLP and a faster folding homolog. However, alphaLP(beta-turn) has impaired proteolytic activity that negates the beneficial folding properties of this variant. This study demonstrates the evolutionary limitations imposed by the simultaneous optimization of folding and functional properties.
Identification of an immunodominant mouse minor histocompatibility antigen (MiHA). T cell response to a single dominant MiHA causes graft-versus-host disease. (1996)

T cell responses to non-MHC antigens are targeted to a restricted number of immunodominant minor histocompatibility antigens whose identity remains elusive. Here we report isolation and sequencing of a novel immunodominant minor histocompatibility antigen presented by H-2Db on the surface of C57BL/6 mouse cells. This nonapeptide (AAPDNRETF) shows strong biologic activity in cytotoxic T lymphocyte sensitization assays at concentrations as low as 10 pM. C3H.SW mice primed with AAPDNRETF in incomplete Freund's adjuvant generated a potent anti-C57BL/6 T cell-mediated cytotoxic activity, and T lymphocytes from AAPDNRETF-primed mice caused graft-versus-host disease when transplanted in irradiated C57BL/6 recipients. These results (a) provide molecular characterization of a mouse dominant minor histocompatibility antigen, (b) identify this peptide as a potential target of graft-versus-host disease and, (c) more importantly, demonstrate that a single dominant minor antigen can cause graft-versus-host disease. These findings open new avenues for the prevention of graft-versus-host disease and should further our understanding of the mechanisms of immunodominance in T cell responses to minor histocompatibility antigens.
Distributed change detection for worms, DDoS and other network attacks (2004)

Self-propagating code (worms) and distributed denial of service (DDoS) attacks are the most frequent and quite devastating attacks on communication networks and the Internet. We provide novel formulations for the rapid detection of these attacks in the control-theoretic framework of change detection. We present algorithms that effectively can detect worms from their temporal spreading characteristics. We describe the effects of the network topology on the algorithms and their performance. We next present algorithms for detecting DDoS while discriminating against changes in the normal traffic. This is accomplished by a distributed detection formalism where a concept of directionality is introduced and exploited. We then turn into attacks to routing protocols in mobile wireless networks. We develop change detection formulations involving hidden Markov models, which match distribution of the number of hops in the mobile and wireless nodes. Using observations that suggest that this distribution is altered substantially in the presence of such attacks we develop and analyze algorithms for their detection.
Supplementary Figure Legends 1-4 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands (2023)

Supplementary Figure Legends 1-4 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands
Minimal Knowledge versus the Real World (2002)

In this paper we show that Viggiano's Minimal Knowledge assumption can be used for color correction when the illumination is known. Indeed, given a known illuminant we find that real data is well modelled by the Minimal Knowledge assumption. Experiments demonstrate that color correction based on the Minimal Knowledge assumption is similar to that based on real data.
CD34+ HSPCs-derived exosomes contain dynamic cargo and promote their migration through functional binding with the homing receptor E-selectin (2023)

Exosomes are tiny vesicles released by cells that carry communications to local and distant locations. Emerging research has revealed the role played by integrins found on the surface of exosomes in delivering information once they reach their destination. But until now, little has been known on the initial upstream steps of the migration process. Using biochemical and imaging approaches, we show here that exosomes isolated from both leukemic and healthy hematopoietic stem/progenitor cells can navigate their way from the cell of origin due to the presence of sialyl Lewis X modifications surface glycoproteins. This, in turn, allows binding to E-selectin at distant sites so the exosomes can deliver their messages. We show that when leukemic exosomes were injected into NSG mice, they traveled to the spleen and spine, sites typical of leukemic cell engraftment. This process, however, was inhibited in mice pre-treated with blocking E-selectin antibodies. Significantly, our proteomic analysis found that among the proteins contained within exosomes are signaling proteins, suggesting that exosomes are trying to deliver active cues to recipient cells that potentially alter their physiology. Intriguingly, the work outlined here also suggests that protein cargo can dynamically change upon exosome binding to receptors such as E-selectin, which thereby could alter the impact it has to regulate the physiology of the recipient cells. Furthermore, as an example of how miRNAs contained in exosomes can influence RNA expression in recipient cells, our analysis showed that miRNAs found in KG1a-derived exosomes target tumor suppressing proteins such as PTEN.
Oncolytic virotherapy – Forging its place in the immunomodulatory paradigm for Multiple Myeloma (2021)

The treatment focus for multiple myeloma (MM) has recently pivoted towards immune modulating strategies, with T-cell redirection therapies currently at the forefront of drug development. Yet, despite this revolution in treatment, MM remains without a sustainable cure. At the same time, tremendous advancement has been made in recombinant and gene editing techniques for oncolytic viruses (OV), which have increased their tumor specificity, improved safety, and enhanced the oncolytic and immunostimulatory potential. These breakthrough developments in oncolytic virotherapy have opened new avenues for OVs to be used in combination with other immune-based therapies such as checkpoint inhibitors, chimeric antigen receptor T-cells (CAR-T) and bispecific T-cell engagers. In this review, the authors place the spotlight on systemic oncolytic virotherapy as an adaptable immunotherapeutic for MM, highlight the unique mechanism of OVs in activating the immune-suppressive marrow microenvironment, and lastly showcase the OV platforms and the promising combination strategies in the pipeline for MM.