Miracle-dz/UniFAR-FTUs huggingface dataset:
ASSESSMENT OF A SYNTHETIC DNA PROBE FOR

Synthetic DNA oligomers homologous to 21-base long repetitive sequences ofPlasmodiumfakiparum DNA were labeled with 32Pusing T4 kinase, and were hybridized with purified DNA and with processed blood samples from Africa. The sequence PFR1, its antiparallel oligomer PFR1R, and PFR1 covalently attached to biotin hybridized sim ilarly to P.fakiparum DNA. One-microliter aliquots of blood from Zaire spotted on prewet nylon filters and hybridized with PFR1 gave detectable autoradiogram signals from samples with parasitemias as low as 1,000 parasites/mm3. Blood lysis and protein digestion followed by alkylation allowed dot-blot processing of larger aliquots of blood. After hybridization with PFR 1 and autoradiography, 26 samples were scored positive visually, compared with 34 scored positive by microscopy. The effective sensitivity for processed l0-@l samples was about 500 parasites/mm3. Signals from hybridized probes were quantitated by liquid scintillation counting and densitometry, and were proportional to the amounts of purified P. fakiparum DNA applied to the filter. Autoradiogram signals also were roughly pro portional (correlation coefficient, r = 0.77) to the number of parasites/mm3 of blood from field samples as determined by microscopic examination. Because of the existence of highly repetitive, species-specific DNA in eukaryotic organisms,' it is anticipated that DNA-based diagnostic probes can be useful diagnostic reagents for para sitic infections. Malaria, Chagas' disease, leish maniasis, and babesiosis are four diseases caused by protozoa for which DNA probes representing repetitive, species-specific sequences have been described.25 The detection of hemoparasites is made somewhat easier because blood contains a relatively low density of host DNA compared to other tissues. Excess host DNA can saturate the binding capacity of filters used in dot-blot pro cessing and therefore decrease the binding of par asite DNA.6 The recent resurgence of malaria7 and the anticipated vaccine studies89 have in tensified the search for methods which can be used for efficient large scale diagnosis of malaria. Specific and sensitive DNA probes could be used
Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep

Motivation Protein-hydroxyapatite interactions govern the development and homeostasis of teeth and bone. Characterization would enable design of peptides to regenerate mineralized tissues and control attachments such as ligaments and dental plaque. Progress has been limited because no available methods produce robust data for assessing phase interfaces. Results We show that tooth enamel pellicle peptides contain subtle sequence similarities that encode hydroxyapatite binding mechanisms, by segregating pellicle peptides from control sequences using our previously developed substitution matrix-based peptide comparison protocol (Oren et al., 2007), with improvements. Sampling diverse matrices, adding biological control sequences, and optimizing matrix refinement algorithms improves discrimination from 0.81 to 0.99 AUC in leave-one-out experiments. Other contemporary methods fail on this problem. We find hydroxyapatite interaction sequence patterns by applying the resulting selected refined matrix (“pellitrix”) to cluster the peptides and build subgroup alignments. We identify putative hydroxyapatite maturation domains by application to enamel biomineralization proteins and prioritize putative novel pellicle peptides identified by In stageTip (iST) mass spectrometry. The sequence comparison protocol outperforms other contemporary options for this small and heterogeneous group, and is generalized for application to any group of peptides. Availability Software to apply this protocol is freely available at github.com/JeremyHorst/Mat4Pep and compbio.org/protinfo/ Mat4Pep. Contact jahorst@gmail.com, ram@compbio.org. Supplementary information Available at Bioinformatics online.
Zr-Based Heusler Compounds for Biomedical Spintronic Applications

Current advances in microelectronics depend on novel approaches based on the synergistic use of charge and spin dynamics of electrons in multi-functional materials. Such new concepts have already found practical applications in magnetoelectronics or spintronics (e.g., spin valves or nonvolatile memory components). For efficient spintronic devices, it is desirable to have an enhanced spin polarization, that, to work with nearly 100% spin-polarized currents. Since half metallic materials have electrons of unique spin polarization around the Fermi level (finite density of states in only one spin channel), they are promising candidates for use as spin injectors in spintronic devices. Although the Heusler compounds reported in the literature presenting half-metallic ferro/ferrimagnetism are numerous, only a few contain elements with low toxicity, as for example zirconium, being also susceptible of convenient preparation and processing. Therefore, in future, zirconium-based compounds could become a much suitable alternative to the presently known cobalt, iron, chromium, titanium, manganese, or scandium-based half-metallic Heusler compounds, being of interest especially in biomedical spintronic related applications involved in corrosive/active environment.
Hydrology of a Southern Appalachian Hypocrene Spring-Fed Fen

Garland Seep is a Southern Appalachian fen that supports a population of federally endangered green pitcher plants (Sarracenia oreophila). The wetland is underlain by clayey stream deposits above fractured bedrock, is located at the base of a mountain slope, and is fed by groundwater that originates as recharge on the adjacent hillslope. Groundwater wells were installed following a hydrologic restoration in the mid-1990s and have been monitored at varying frequencies since that time. The 20+ year record provides evidence that Garland Seep can be classified as a “hypocrene fen,” in which spring flow rarely reaches the ground surface because of low discharge rates and high evapotranspiration (ET). In general, water-level fluctuations followed seasonal ET patterns, with higher water levels in the winter and early spring (when ET is low) and lower levels in the summer and fall. During wetter years, the water table remained near the ground surface for much of the year, with the clay layer underlying the site retaining moisture even after water levels had dropped. The “clay wetting” period was shorter during dryer years and corresponded with a reduction in the number of pitcher plant clumps observed at the site. In addition to the geologic and climatic controls on hydrology, previous landowners used fire to maintain open space for grazing, and The Nature Conservancy has continued the practice to combat woody vegetation and to open the canopy. Prescribed burns reduce ET (at least initially), cause a rise in water levels, and have helped maintain a thriving Sarracenia population.
Social desirability and cynicism biases in CSR surveys: an empirical study of hotels

Purpose: Previous studies support the notion that corporate social responsibility (CSR) initiatives can have a positive effect on customers in the hospitality and tourism industry. However, most of these studies have ignored response biases and none have incorporated them into their analyses numerically. This study aims at closing this research gap. Design/methodology/approach: We utilized a hybrid choice model to test for the hypothesized effects of social desirability (SD) and cynicism biases on reported purchase intention. We further compared the results with those of analyses that ignore these biases to demonstrate their distorting influence. Findings: Our results indicate that SD and cynicism biases have a moderating effect on reported purchase intention. Older generations and frequent travelers seem particularly prone to bias, and the biases have a distorting effect on the overall survey results. Research limitations/implications: Traditional analyses that exclude biases, incorrectly, suggest several aspects of CSR that are significant (or insignificant) to purchase intention and provide unreliable results. We did not generalize bias-prone respondent segments but urge future research to investigate this. Practical implications: Hotel managers aspiring to gain competitive advantage through CSR investment must consider biases in their market research. Otherwise, they risk developing CSR initiatives that do not instigate positive customer behaviors, leading to the failure of the investment. Originality/value: We quantified SD and cynicism as significant causes of response bias, which distorts survey results. Previous studies have conceptualized SD without quantifying its impact, while cynicism has been identified as a novel source of bias in the industry. This study further introduces hybrid choice modeling as a novel approach to address response bias that could extend itself beyond the industry studied here.
Heterogeneity of Stress Field in NE Japan and Implications for Fault Strength and Earthquake Occurrence Mechanism

The state of stress in the Earth’s crust is a key to understanding crustal dynamics. Recent seismological observations in NE Japan clearly show spatial variations of stress orientations in the crust; the stress ﬁeld is basically consistent with relative plate motions as a ﬁrst-order approximation, but it rotates signiﬁcantly beneath mountain ranges or in and around the source regions of large earthquakes. Such observations suggest that the deviatoric stress ﬁeld produced by relative plate motions is small enough to be disturbed by other stress sources such as topography and earthquake faulting. According to quantitative modeling studies, the deviatoric stress magnitude in the seismogenic zone in NE Japan should be in the order of tens of MPa, which is too small to overcome laboratory-derived fault strength. This suggests that fault weakening mechanisms, including the low frictional coefﬁcient of the fault surface and overpressurized ﬂuids, play an important role in the generation of earthquakes. Deviatoric stress magnitude in seismogeneic zones can be lower than in stable continents if the fault weakening mechanism is related to the subduction process. Given that deviatoric stress magnitude is generally small in the seismogeneic zones of island arcs, various stress sources can lead to heterogeneous states of stress. It is important to take account of stress heterogeneity when modeling crustal dynamics.
Novel Materials for Combined Nitrogen Dioxide and Formaldehyde Pollution Control under Ambient Conditions

Formaldehyde (HCHO) and nitrogen dioxide (NO2) often co-exist in urban environments at levels that are hazardous to health. There is a demand for a solution to the problem of their combined removal. In this paper, we investigate catalysts, adsorbents and composites for their removal efficiency (RE) toward HCHO and NO2, in the context of creating a pollution control device (PCD). Proton-transfer-reaction mass spectrometry and cavity ring-down spectrometry are used to measure HCHO, and chemiluminescence and absorbance-based monitors for NO2. Commercially available and lab-synthesized materials are tested under relevant conditions. None of the commercial adsorbents are effective for HCHO removal, whereas two metal oxide-based catalysts are highly effective, with REs of 81 ± 4% and 82 ± 1%, an improvement on previous materials tested under similar conditions. The best performing material for combined removal is a novel composite consisting of a noble metal catalyst supported on a metal oxide, combined with a treated active carbon adsorbent. The composite is theorized to work synergistically to physisorb and oxidize HCHO and chemisorb NO2. It has an HCHO RE of 72 ± 2% and an NO2 RE of 96 ± 2%. This material has potential as the active component in PCDs used to reduce personal pollution exposure.
Development of a Mathematical Model to Understand, Design & Improve Oncolytic Virus Therapies

Oncolytic viruses (OVs) are emerging as a potent therapeutic platform for the treatment of malignant disease. The tumor cells inability to induce antiviral defences in response to a small cytokine known as interferon (IFN) is a common defect exploited by OVs. Heterogeneity in IFN signalling across tumors is therefore a pillar element of resistance to these therapies. I have generated a mathematical model and simulation platform to study the impact of IFN on OV dynamics in normal and cancerous tissues. In the first part of my thesis, I used this model to identify novel OV engineering strategies which could be implemented to overcome IFN based resistance in tumor tissues. From these simulations, it appears that a positive feedback loop, established by virus-mediated expression of an interferon-binding decoy receptor, could increase tumor cytotoxicity without compromising normal cells. The predictions set forth by this model have been validated both qualitatively and quantitatively in in-vitro and in-vivo models using two independent OV strains. This model has subsequently been used to investigate OV attenuation mechanisms, the impact of tumor cell heterogeneity, as well as drug-OV interactions. Following these results, it became apparent that selectivity should equally be observed when overwhelming the cell with a non replicating virus. While normal tissues will clear this pseudoinfection rapidly, owing to their high baseline in antiviral products at the onset of infection, tumor cells with defective anti-viral pathways should not have readily available biomachinery required to degrade this pro-apoptotic signal. Recapitulated by the mathematical model, nonreplicating virus-derived particles generated by means of UV irradiation selectively kill tumor cells in cultured cell lines and patient samples, leading to long term cures in murine models. Taken together, this thesis uses a novel mathematical model and simulation platform to understand, design & improve oncolytic virus-based therapeutics.
Beyond the traditional simulation design for evaluating type 1 error rate: from ‘theoretical’ to ‘empirical’ null

When evaluating a newly developed statistical test, the first step is to check its type 1 error (TIE) control using simulations. This is often achieved by the standard simulation design S0 under the so-called ‘theoretical’ null of no association. In practice, whole-genome association analyses scan through a large number of genetic markers (Gs) for the ones associated with an outcome of interest (Y), where Y comes from an unknown alternative while the majority of Gs are not associated with Y, that is under the ‘empirical’ null. This reality can be better represented by two other simulation designs, where design S1.1 simulates Y from an alternative model based on G then evaluates its association with independently generated Gnew, while design S1.2 evaluates the association between permutated Yperm and G. More than a decade ago, Efron (2004) has noted the important distinction between the ‘theoretical’ and ‘empirical’ null in false discovery rate control. Using scale tests for variance heterogeneity and location tests of interaction effect as two examples, here we show that not all null simulation designs are equal. In examining the accuracy of a likelihood ratio test, while simulation design S0 shows the method has the correct T1E control, designs S1.1 and S1.2 suggest otherwise with empirical T1E values of 0.07 for the 0.05 nominal level. And the inflation becomes more severe at the tail and does not diminish as sample size increases. This is an important observation that calls for new practices for methods evaluation and interpretation of T1E control.
RIGOUR AND PROOF

Abstract This paper puts forward a new account of rigorous mathematical proof and its epistemology. One novel feature is a focus on how the skill of reading and writing valid proofs is learnt, as a way of understanding what validity itself amounts to. The account is used to address two current questions in the literature: that of how mathematicians are so good at resolving disputes about validity, and that of whether rigorous proofs are necessarily formalizable.
Evaluating Reproductive Strategies and Female Bateman Gradients in Ditrema temminckii: Is the Number of Fathers a Good Approximation for the Number of Mates?

Surfperches (Embiotocidae) are a unique family of viviparous fishes that have internal fertilization, gestation to the sub-adult stage, and live-birth; therefore, maternal investment is extremely high. This invokes the expectation that brood size is limited and females should be choosy and select few mates. Yet multiple paternity occurs in all eight species examined to date, with high prevalence ranging from 92–100%. Most surfperches are found along the Eastern Pacific coast, but Ditrema temminckii is distributed in the Western Pacific and we found differences in their mating strategy compared to other surfperches. In D. temminckii, prevalence of multiple paternity was only 60%. Further, the average number of sires was only 1.86 per brood even though brood sizes ranged from 12–45, and paternity was skewed, with the majority of paternity allocated to a single male. We propose that these differences may be associated with strong female selection on males in this species. Finally, we evaluated whether the number of fathers is an accurate estimate for the number of mates by comparing the number of alleles detected from fathers within the brood to the number of alleles from mates via genotyping alleles from spermatozoa within the uterine sac and found no significant difference, suggesting that the number of sires is a reasonable estimate for the number of mates in D. temminckii.
Bioelectronic control of chloride ions and concentration with Ag/AgCl contacts

Translation between ionic currents and measurable electronic signals is essential for the integration of natural systems and artificial bioelectronic devices. Chloride ions (Cl−) play a pivotal role in bioelectricity, and they are involved in several brain pathologies, including epilepsy and disorders of the autistic spectra, as well as cancer and birth defects. As such, controlling [Cl−] in solution can actively influence biochemical processes and can be used in bioelectronic therapies. Here, we demonstrate a bioelectronic device that uses Ag/AgCl contacts to control [Cl−] in solution by electronic means. We do so by exploiting the potential dependence of the reversible reaction, Ag + Cl− ↔ AgCl + e−, at the contact/solution interface, which is at the basis of the well-known Ag/AgCl reference electrode. In short, a negative potential on the Ag/AgCl contact transfers Cl− from the contact to the solution with increasing [Cl−] and vice versa. With this strategy, we demonstrate precise spatiotemporal control of [Cl−] in solution that can be used to affect physiological processes that are dependent on [Cl−]. As proof-of-concept, we use [Cl−] control to influence the membrane voltage on human pluripotent stem cells.
Correlations between fish assemblage structure and environmental variables of the Seti Gandaki River Basin, Nepal

ABSTRACT This paper addresses the relationship between fish and environmental variables from the Seti Gandaki River Pokhara, Nepal. The water bodies previously had higher abundance and distribution of fishes, which are declining probably due to deterioration of abiotic characteristics and degradation of habitat. Five study sites were: three along the main channel and two along the tributaries. Water sampling was conducted fortnightly and fish sampling was done monthly. Altogether 30 species of fishes belonging to 5 orders, 9 families and 24 genera were recorded. The redundancy analysis (RDA) revealed significant correlations between fish assemblage and environmental variables. The first two axes accounted for 44.15% of the variation of which RDA1 explained 30.32% and correlated with conductivity, pH, dissolved oxygen, free carbon dioxide, ortho-phosphate, nitrite and silicates; while RDA2 explained 13.83% and correlated with depth, width, discharge and nitrates. Likewise, RDA1 revealed a gradient from species that require more oxygenated waters of upstream sites (Schizothorax richardsonii, Pseudecheneis eddsi, Naziritor chelynoides, Garra annandalei, Schistura rupecula and Lepidocephalichthys guntea) to less oxygenated urban and downstream sites (Puntius sophore, Pethia conchonius, Barilius bendelisis, Barilius vagra, Garra gotyla, Mastacembelus armatus and Channa orientalis). RDA2 revealed the gradient from species inhabiting urban and downstream sites to upstream sites.
Tinjauan Kasus Model Speech Recognition: Hidden Markov Model

Abstrak— Teknologi pengenal suara (speech recognition) merupakan teknologi yang berkembang pesat dalam bidang kecerdasan buatan (artificial intelligent). Saat ini, teknologi pengenal suara menjadi hal yang komersil melalui berbagai media teknologi seperti smartphone dan komputer. Salah satu pembentuk struktur pengenal suara agar dapat bekerja pada perangkat tersebut adalah model statistik pengenal suara Hidden Markov Model (HMM). Penerapan HMM pada berbagai kasus menunjukkan bahwa model ini cocok dengan berbagai macam data. Tulisan ini merupakan sebuah tinjauan untuk model HMM yang bertujuan untuk memberikan gambaran dan pemahaman terhadap kinerja HMM melalui rangkuman sejumlah penelitian yang digunakan dalam berbagai data. Penerapan HMM tersebut menunjukkan optimalisasi kinerja HMM dan tinjauan terhadap sejumlah penelitian menunjukkan bahwa tingkat keberhasilan HMM dalam mengenali data mencapai 71.43%. Kata kunci— Speech recognition, artificial intelligent, model statistik, hidden markov model, media teknologi
Identification of Polynucleotide Phosphorylase (PNPase) in Escherichia coli Involved in Persister Formation

Despite the identification of many genes and pathways involved in the persistence phenomenon of bacteria, the mechanisms of persistence are not well understood. Here, using Escherichia coli as a model, we identified polynucleotide phosphorylase (PNPase) as a key regulator in persister formation. We successfully constructed pnp knockout mutant strain and its complemented strain, and exposed the pnp knockout mutant and complemented strain to antibiotics and stress conditions. The results showed that, compared with the wild-type W3110, the pnp knockout strain had defect in persistence to antibiotics and stress conditions, and the persistence to antibiotics and stresses was restored upon complementation. RNA-Seq was performed to identify the transcriptome profile in the pnp knockout strain compared with wild-type strain W3110, and the data revealed that 242 (166 up-regulated, and 76 down-regulated) genes were differentially expressed in the pnp knockout mutant strain. KEGG pathway analysis of the up-regulated genes showed that they were mostly mapped to metabolism and virulence pathways, most of which are positively regulated by the global regulator cyclic AMP receptor protein (CRP). Similarly, the transcription level of the crp gene in the pnp-deletion strain increased 3.22-fold in the early stationary phase. We further explored the indicators of cellular metabolism of the pnp-deletion strain, the persistence phenotype of the pnp and crp double-deletion mutant, and the transcriptional activity of crp gene. Our results indicate that PNPase controls cellular metabolism by negatively regulating the crp operon at the post-transcriptional level by targeting the 5’- Untranslated Region (UTR) of the crp transcript. This study offers new insight about the persister mechanisms and provides new targets for development of new drugs against persisters for more effective treatment of persistent bacterial infections.