jimnoneill/paper-to-field-training huggingface dataset:
Erratum to: microRNA machinery is an integral component of drug-induced transcription inhibition in HIV-1 infection.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

RNA interference plays a significant role in manipulating cellular and viral mechanisms to maintain latency during HIV-1 infection. HIV-1 produces several microRNAs including one from the TAR element which alter the host's response to infection. Since cyclin/cdk complexes are important for viral transcription, these studies focus on the possible cdk inhibitors that inhibit viral transcription, without affecting normal cellular mechanisms. Roscovitine and Flavopiridol are well-studied cdk inhibitors that are effective at suppressing their target cdks at a low IC50. These cdk inhibitors and possibly future generations of drugs are affected by microRNA mechanisms. From our studies, we developed a third generation derivative called CR8#13. In cells that lack Dicer there was a higher level of basal viral LTR-reporter transcription. When drugs, specifically Flavopiridol and CR8#13 were added, the transcriptional inhibition of the LTR was less potent in cells that lacked Dicer. Also, after transfection with HIV-1 clone (pNL4.3), CR8 and CR8#13 derivatives were shown to be more effective viral transcription inhibitors in cell lines that contained Dicer (T-cells) as compared to Dicer deficient lines (monocytes). We next asked whether the addition of CR8 or CR8#13 could possibly increase levels of TAR microRNA in HIV-1 LTR containing cells. We demonstrate that the 3'TAR microRNA is produced in higher amounts after drug treatment, resulting in microRNA recruitment to the LTR. MicroRNA recruitment results in chromatin alteration, changes in Pol II phosphorylation and viral transcription inhibition. In conclusion, our results indicate that viral microRNA, specifically the TAR microRNA produced from the HIV-1 LTR is responsible for maintaining latent infections by manipulating host cell mechanisms to limit transcription from the viral LTR promoter. With the microRNA machinery present, cdk inhibitors are able to significantly increase the amount of TAR microRNA, leading to downregulation of viral LTR transcription.
Some necessary conditions for a critical velocity interaction between the ionospheric plasma and a xenon cloud

Field: Physics and Astronomy (Physical Sciences)

The conditions for an experiment to study the critical ionization velocity effect in the interaction between a Xenon cloud, released from a satellite, and the ionospheric plasma are investigated. The model used is based on the assumption that there exists an effective process that transfers the energy, that is available in the relative motion, to the electrons. Some necessary conditions to obtain significant heating or deceleration of the plasma penetrating the cloud are calculated. The conditions are mainly given by the energy available in the relative motion and the rates of the different binary collision processes involved. As the released gas cloud expands the possibilities for a critical velocity interaction will exist only within a certain range of cloud radii. It is shown that the charge transfer collision cross section between the ionospheric ions and the cloud atoms is an important parameter and that Xenon is a very suitable gas in that respect.
High throughput quantitation of artesunate and its degradation products by flow injection gradient ratio standard addition mass spectrometry (FI-GRSA-MS)

Field: Chemistry (Physical Sciences)

There is a pressing need to equip post-marketing drug quality surveillance systems with higher throughput and robust analytical tools that can reinforce pharmaceutical quality control to ensure safety of patients and integrity of treatment practices. This manuscript reports the development of a flow injection analysis mass spectrometry-based gradient ratio standard addition (FI-GRSA-MS) method for quantification of artesunate, a common antimalarial active pharmaceutical ingredient in a simple, efficient, accurate, and high throughput manner. Dodecylamine (DDA) was evaluated as an electrospray modifier for improving the sensitivity of the GRSA quantitation method. The linear dynamic range and precision for artesunate quantification were found to be 7 ng to 86 pg artesunate and 2.1%, respectively. When compared to high performance liquid chromatography, results were found to be equivalent at the 95% confidence level. To identify chemical markers of improper drug storage and artesunate degradation, tablets were artificially exposed to heat for time periods ranging between 1 and 12 hours and the degradation products detected were identified via accurate mass and isotopic cluster abundance measurements. Moreover, degradation behavior of artesunate tablets from two different manufacturers under identical degradation conditions was investigated, indicating that tablet formulation plays a significant role in the shelf life of these valuable medicines.
Drug target time tracking

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Our recent paper compared&nbsp; parameters from a commercial database with related data from the public domain.&nbsp; Since then I explored the open publication sources a bit more to see what one can get out if you don't have a commercial source, or you just want a corroborative check. As an example&nbsp; I found the following&nbsp; simple PubMed plot of two classic drug target types quite impressive
Nonstationarity and 1/f noise characteristics in heart rate

Field: Medicine (Health Sciences)

The power spectrum of human heart rate (HR) measured over 24 h exhibits “power-law” 1/ f α -type spectral behavior with α ≈ 1. We investigate possible nonstationarity in time of the exponent α using maximum likelihood estimation, which allows relatively short data segments to be used. Examination of 24-h HR records from ambulatory normal and congestive heart failure (CHF) subjects indicates that the power-law structure of HR is nonstationary. In addition, α varies with time scale and is different for normal (α ≈ 1) and CHF (α ≈ 1.5) subjects. Simulations suggest that a possible mechanism underlying the observed power-law spectrum may be a switching between values of α near zero (white noise) and near two (Brownian motion). This mechanism generates power-law forms quantitatively similar to CHF subjects when the switching occurs very rapidly and similar to normal subjects when the switching is less rapid.
The Cambium and its Derivative Tissues Problems in Identifying the Wood of Mesozoic Coniferae

Field: Agricultural and Biological Sciences (Life Sciences)

Journal Article The Cambium and its Derivative Tissues Problems in Identifying the Wood of Mesozoic Coniferae Get access I. W. BAILEY I. W. BAILEY Arnold Arboretum, Harvard University, and Division of Plant Biology, Carnegie Institution of Washington Search for other works by this author on: Oxford Academic PubMed Google Scholar Annals of Botany, Volume os-47, Issue 1, January 1933, Pages 145–157, https://doi.org/10.1093/oxfordjournals.aob.a090370 Published: 01 January 1933
Coexistent Vestibular Schwannoma and Creutzfeldt–Jakob Disease: Recognition and Infection Control

Field: Medicine (Health Sciences)

Objectives: We describe the first known case of coexistent vestibular schwannoma (VS) and Creutzfeldt–Jakob disease (CJD). Our objectives are to use this case as a general lesson for the subspecialist otolaryngologist to remain vigilant to alternative diagnoses, and to specifically improve understanding of the diagnosis and management of CJD as relevant to the practice of otolaryngology and skull base surgery. Methods: Retrospective case review performed in June 2016 at an academic, tertiary, referral center. Results: A 55-year-old man presents with one month of worsening disequilibrium and short-term memory loss. Magnetic resonance imaging (MRI) (T1, T2) identified a 4 mm left VS which was then surgically resected. Postoperatively, his neurological status decline continued, and subsequent MRI identified patterns of FLAIR hyperintensity and diffusion restriction consistent with CJD. While CSF analysis (tau and 14-3-3) and EEG was inconclusive, serial imaging and the clinical course were highly suggestive of CJD. A probable diagnosis was made, surgical instruments quarantined, and infection control involved to minimize transmission risk. The patient died 6 months after symptom onset. Conclusions: Patients with CJD may initially present with otolaryngologic symptoms. MRI signal abnormality in the basal ganglia on diffusion weighted imaging and FLAIR sequences in conjunction with physical findings and clinical course may help make a probable diagnosis CJD. Prions are resistant to traditional sterilization and additional measures must be taken to prevent iatrogenic transmission. Level of Evidence: Level 4—Case series
Evaluation of rapid alternative methods for drug susceptibility testing in clinical isolates of Mycobacterium tuberculosis. Mem. Inst. Oswaldo Cruz 101:535–542

Field: Medicine (Health Sciences)

A study was carried out to compare the performance of a commercial method (MGIT) and four inexpensive drug susceptibility methods: nitrate reductase assay (NRA), microscopic observation drug susceptibility (MODS) assay, MTT test, and broth microdilution method (BMM). A total of 64 clinical isolates of Mycobacterium tuberculosis were studied. The Lowenstein-Jensen proportion method (PM) was used as gold standard. MGIT, NRA, MODS, and MTT results were available on an average of less than 10 days, whereas BMM results could be reported in about 20 days. Most of the evaluated tests showed excellent performance for isoniazid and rifampicin, with sensitivity and specificity values&gt; 90%. With most of the assays, sensitivity for ethambutol was low (62-87%) whereas for strepto-mycin, sensitivity values ranged from 84 to 100%; NRA-discrepancies were associated with cultures with a low proportion of EMB-resistant organisms while most discrepancies with quantitative tests (MMT and BMM) were seen with isolates whose minimal inhibitory concentrations fell close the cutoff. MGIT is reliable but still expensive. NRA is the most inexpensive and easiest method to perform without changing the organization of the routine PM laboratory performance. While MODS, MTT, and BMM, have the disadvantage from the point of view of biosafety, they offer the possibility of detecting partial resistant strains. This study shows a very good level of agreement of the four low-cost methods compared to the PM for rapid detection of isoniazid, rifampicin and streptomycin resistance (Kappa values&gt; 0.8); more standardization is needed for ethambutol. Key words: drug-susceptibility testing- Mycobacterium tuberculosis- rapid methods The emergence of tuberculosis in conjunction with the increasing number of multi-drug resistant strains of Mycobacterium tuberculosis has increased the need for rapid and reliable methods of diagnosis and drug suscep-tibility testing (DST). The Lowenstein-Jensen (LJ) or agar proportion
Utility and bias in psychosocial evaluations for transplant listing

Field: Medicine (Health Sciences)

Purpose of review Disparities in access to transplantation are persistent and pervasive among minoritized populations, and remain incompletely explained by socioeconomic status, insurance, geography, or medical factors. Although much attention has been paid to factors contributing to disparities in organ allocation, fewer studies have focused on barriers to the transplant waitlist. Given increasing calls for equity in organ transplantation, we examine the role of nonmedical factors used in transplant listing decisions, including psychosocial factors like social support, motivation, and knowledge in improving utility in transplant listing decisions, as well as their potential for reinforcing bias. Recent findings Minoritized groups are more likely to be declined from transplant listing owing to psychosocial criteria. Lack of consistent definitions, screening tools with differential subgroup validity, and insufficient evidence-base contribute to concerns about reliance on psychosocial factors in transplant listing decisions. Summary Improving consistency and evidence-based approaches in patient evaluation and listing decisions will require greater efforts to identify which psychosocial risk factors are predictive of posttransplant outcomes. Social needs screening presents a strengths-based framework for incorporating psychosocial factors in transplant listing decisions.
Improvement of DBSCAN Algorithm Involving Automatic Parameters Estimation and Curvature Analysis in 3D Point Cloud of Piled Pipe

Field: Computer Science (Physical Sciences)

Bin-picking in the industrial area is a challenging task since the object is piled in a box. The rapid development of 3D point cloud data in the bin-picking task has not fully addressed the robustness issue of handling objects in every circumstance of piled objects. Density-Based Spatial Clustering of Application with Noise (DBSCAN) as the algorithm that attempts to solve by its density still has a disadvantage like parameter-tuning and ignoring the unique shape of an object. This paper proposes a solution by providing curvature analysis in each point data to represent the shape of an object therefore called Curvature-Density-Based Spatial Clustering of Application with Noise (CVR-DBSCAN). Our improvement uses curvature to analyze object shapes in different placements and automatically estimates parameters like Eps and MinPts. Divided by three algorithms, we call it Auto-DBSCAN, CVR-DBSCAN-Avg, and CVR-DBSCAN-Disc. By using real-scanned Time-of-Flight camera datasets separated by three piled conditions that are well separated, well piled, and arbitrary piled to analyze all possibilities in placing objects. As a result, in well separated, Auto-DBSCAN leads by the stability and accuracy in 99.67% which draws as the DBSCAN using specified parameters. For well piled, CVR-DBSCAN-Avg gives the highest stability although the accuracy can be met with DBSCAN on specified parameters in 98.83%. Last, in arbitrary piled though CVR-DBSCAN-Avg in accuracy lower than DBSCAN which is 73.17% compared to 80.43% the stability is slightly higher with less outlier value. Deal with computational time higher than novel DBSCAN, our improvement made the simplicity and deep analysis in scene understanding.
[The influence of extracellular pH on volume-activated chloride current in the prostate cancer epithelial cells].

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The influence of extracellular pH on characteristics of volume-activated chloride current, ICl,swell, in the human prostate cancer epithelial cell line, LNCaP, was studied using the patch-clamp technique. Acidification of the extracellular hypotonic solution used to develop the current shortened the temporal parameters of ICl,swell development and reduced its maximal density. Sudden shifts of the pH towards acidification caused fast, transient potentiation of the current followed by its sustained inhibition. Voltage-dependent inactivation of ICl,swell was the most pronounced in the narrow range of pH = 6-7. Based on the analysis of our data we hypothesize that volume-regulated anion channels underlying ICl,swell possess in their structure at least two pH-sensitive molecular groups with similar pK = 6, titration of which modulates the current amplitude and two additional proton-sensitive groups that determine channel's inactivation.
Dictatorship, liberalism and the Pareto rule: Possible and impossible

Field: Economics, Econometrics and Finance (Social Sciences)

The current economic crisis has shaken belief in the capacity of neoliberal 'free market' policies. Numerous supports of state intervention have arisen, and the interest for social choice theory has revived. In this paper we consider three standard properties for aggregating individual into social preferences: dictatorship, liberalism and the Pareto rule, and their formal negations. The context of the pure first-order classical logic makes it possible to show how some combinations of the above mentioned conditions, under the hypothesis of unrestricted domain, form simple and reasonable examples of possible or impossible social choice systems. Due to their simplicity, these examples, including the famous 'liberal paradox', could have a particular didactic value.
Protein and Protein Replacers for Dairy Cattle

Field: Agricultural and Biological Sciences (Life Sciences)

The common standards for feeding dairy cattle in the U.S. and Canada are those based upon the1971 edition of Nutrient Requirements of Dairy Cattle (NRC- ISBN 0-309-01916-8), or, the 22ndedition of Feeds and Feeding (Morrison, 1956-nolonger in print; 9th edition, ab1idged of same work,1962, is still available and contains same tabular material). The NRC data is based upon consideration of the amounts of crude protein and digestible protein for dairy animals of various ages, physiological status, and production, whereas the Morrison values are based solely on digestible protein, on the same considerations.
It is well-known that a lack of protein will depress perfo1mance of animals, and in dairy cattle a severe lack will lower not only the yield of lactating cows, but also will affect the solids not-fat content of the milk. A large excess of protein, on the other hand, is not toxic but is uneconomical, particularly at present-day prices for protein ingredients (or their substitutes). A high level of protein may increase milk protein slightly, but does not increase milk yield, provide the animals already receive required minimal levels.
In general, the present NRC requirements for milk production furnish about 150% of the amount of crude protein in the milk. The Morrison standards are not set figures but give range values, and these are about 130-165% of the protein in the milk produced.
Personally, my belief is that calculation of needs on the basis of DP is far superior to a system based upon CP.
When considering protein requirements of cattle it is necessary to remember that well-fed dairy animals have the ability to store protein, particularly during the dry period, and then they are able to catabolize body protein stores to synthesize milk during lactation. Naturally, the degree to which this is done is dependent upon many factors, but it is of critical value when high-producing cows are incapable of consuming enough feed to meet both their protein and energy needs during early lactation.
Topological Map: Minimal Encoding of 3d Segmented Images

Field: Computer Science (Physical Sciences)

In this paper we define formally and completely the 3d topological map introduced in BertrandAl00: a model which encodes totally and minimally all the topological information of a 3d image. In particular, we focus on the problem of disconnections induced by the constructive definition based on several levels of maps. This multilevel representation is more or less a graph pyramid in sense that each level can be compute from the previous one in term of merge operations. Furthermore, algorithms extracting these maps from a segmented image have been given in BertrandAl00 and have been implemented and tested in practical applications.
Ramp function regression: a tool for quantifying climate

Field: Earth and Planetary Sciences (Physical Sciences)

A method is proposed for fitting a ‘ramp’ to measured data. This is a continuous function, segmented in three parts: x fitOtUax1 for tRt1, x2 for trt2, and linearly connected between t1 and t2. Its purpose is to measure transitions in the mean of time series as they occur, for example, in paleoclimatic records. The unknowns x1 and x2 are estimated by weighted least-squares regression, t1 and t2 by a brute-force search. Computing costs are reduced by several methods. The presented Fortran 77 program, RAMPFIT, includes analysis of weighted ordinary residuals for checking the validity of the ramp form and other assumptions. It fits an AR(1) model to the residuals to measure serial dependency; uneven time spacing is thereby allowed. Three bootstrap resampling schemes (nonparametric stationary, parametric, and wild) provide uncertainties for the estimated parameters. RAMPFIT works interactively (calculation/visualization). Example time series (one artificial, three measured) demonstrate that this approach is useful for practical applications in geosciences (n less than a few hundred, noise, unevenly spaced times), and that the ramp function may serve well to model climate transitions. # 2000 Elsevier Science Ltd. All rights reserved.
Synthesis, spectral studies and antibacterial activity of iron(III) complexes with hydrazone functionalized ligands: X-Ray structure determination of a novel five coordinate complex containing labile ligands

Field: Chemistry (Physical Sciences)

Iron(III) complexes having general formula FeLCl2 [where, L = 2-acetylpyridine acetoylhydrazone(APAH), 2-acetylpyridine benzoylhydrazone(APBH), 2-acetylthiophene acetoylhydrazone(ATAH), and 2-acetythiophene benzoylhydrazone(ATBH) ] have been synthesized characterized based on molar conductivity, electronic and IR spectroscopy. The structure of iron(III) complex with APBH ligand is determined using single crystal X-Ray crystallography . The complex crystallizes in monoclinic space group P21/n with a = 7.8490(6) Å, b = 15.1018(11) Å, c = 13.2263(10) Å, α = 90°, β=100.183(3)°, γ = 90°, V = 1543.1(2) Å3 and Z = 4 with central Fe(III) ion coordinated one tridentate APBH ligand. The iron is 5- coordinate binding with one organic (hydrazone) unit and two labile chloride ligands. The hydrazone acts as NNO –tridentate donor system. Iron is coordinated by pyridine ring nitrogen, azomethine nitrogen and benzoyl oxygen atoms and the two chloride ligands bind with metal completing distorted square pyramidal structure. The iron complexes are screened for their anti-bacterial activities against Pseudomonas aureoginos and Bacillus cereus Acetoyl hydrazones show more antibacterial activity than the corresponding benzoyl hydrazones. Functional groups of azomethine carbon are varied. The hydrazones having a methyl/ and pyridine groups show more anti bacterial activity. The complexes show more activity than the ligands.
Multiple cutaneous reticulohistiocytosis with T‐cell large granular lymphocyte clonopathy

Field: Medicine (Health Sciences)

Abstract A 63‐year‐old Caucasian man presented with a 4‐month history of disseminated asymptomatic reddish‐brown papulonodular lesions. A skin biopsy showed dermal infiltration with CD 68 + histiocytes, predominantly with eosinophilic cytoplasm, some with a ground‐glass cytoplasm, and a small number of giant cells. The diagnosis of multiple cutaneous reticulohistiocytosis was made. Bone marrow immunophenotyping due to peripheral blood lymphocytosis revealed the presence of a monoclonal population of CD 3 + , CD 8 + CD 57 + large granular lymphocytes. The present case suggests the coexistence of multiple cutaneous reticulohistiocytosis with an underlying disorder.