gebhart/patrepeval huggingface dataset:
Acidogenic Fermentation of Brewers’ Spent Grain Monitored through Two-Dimensional Fluorescence Spectroscopy (2023)

Biological systems are commonly controlled and monitored through offline and time-consuming tools, which often impairs an effective and real-time response to counteract system disturbances. The feasibility of using two-dimensional (2D) fluorescence spectroscopy as a non-invasive, non-destructive, and real-time procedure to monitor the acidogenic fermentation of brewer’s spent grain (BSG) in a granular sludge reactor was evaluated. For that, the effect of pH fluctuations on the system response was used as a model to ascertain the 2D fluorescence spectroscopy applicability to monitor the process performance, namely, to predict the fermentation products (FP) and the soluble protein (SProt) concentrations in the effluent stream through mathematical analysis. The pH fluctuations over the course of the reactor’s operation altered the granules’ microbiome composition, leading to different effluent FP profiles. Fluorescence excitation–emission matrices (EEMs) were used with projection to latent structures (PLS) modeling to predict the FP and SProt concentrations in the effluent with average errors below 0.75 and 0.43 g L–1, respectively. Both models were able to capture the tendency of the data even when the accuracy of prediction was not so high. The combined approach of using 2D fluorescence spectroscopy and mathematical analysis seemed promising for real-time monitoring of the acidogenic fermentation of complex substrates.
2-Dehydrococcinelline, a New Defensive Alkaloid from the Ladybird Beetle <i>Anatis ocellata</i> (Coccinellidae) (1997)

2-Dehydrococcinelline (6), a novel coccinellid defensive alkaloid, has been isolated from the European ladybird Anatis ocellata. Its structure was established by spectroscopic methods and confirmed by chemical correlation with precoccinelline (1).
Xenbase: expansion and updates of the Xenopus model organism database (2012)

Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and Xenopus data to workers using other model organisms. As an amphibian Xenopus serves as a useful evolutionary bridge between invertebrates and more complex vertebrates such as birds and mammals. Xenbase content is collated from a variety of external sources using automated and semi-automated pipelines then processed via a combination of automated and manual annotation. A link-matching system allows for the wide variety of synonyms used to describe biological data on unique features, such as a gene or an anatomical entity, to be used by the database in an equivalent manner. Recent updates to the database include the Xenopus laevis genome, a new Xenopus tropicalis genome build, epigenomic data, collections of RNA and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module that contains data on over 700 antibodies that are useful for exploring Xenopus cell and developmental biology.
The impact of genetic diversity on gene essentiality within the <i>E. coli</i> species (2020)

Abstract Bacteria from the same species can differ widely in their gene content. In E. coli , the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ∼3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains’ phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics.
Biologically inspired analogue signal processing: Some results towards developing next generation signal analyzers (2009)

In this work we describe the possibility of designing an analogue signal analyzer taking inspiration from biological and chemical information processing methodology present in the nature. The principal component of such a system is an adaptive-frequency Hopf oscillator. Using the proposed methodology it is possible to carry out Fourier as well as time-frequency analysis of a signal (similar to wavelet analysis) without changing the underlying circuit structure. This work may provide a route to a computationally superior and less power consuming next-generation signal processing system. Some open issues for making such an approach to practice are also discussed.
Immune-Mediated Inhibition of Metastases after Treatment with Local Radiation and CTLA-4 Blockade in a Mouse Model of Breast Cancer (2005)

The combination of local RT with CTLA-4 blockade is a promising new immunotherapeutic strategy against poorly immunogenic metastatic cancers.
Complement as driver of systemic inflammation and organ failure in trauma, burn, and sepsis (2021)

Complement is one of the most ancient defense systems. It gets strongly activated immediately after acute injuries like trauma, burn, or sepsis and helps to initiate regeneration. However, uncontrolled complement activation contributes to disease progression instead of supporting healing. Such effects are perceptible not only at the site of injury but also systemically, leading to systemic activation of other intravascular cascade systems eventually causing dysfunction of several vital organs. Understanding the complement pathomechanism and its interplay with other systems is a strict requirement for exploring novel therapeutic intervention routes. Ex vivo models exploring the cross-talk with other systems are rather limited, which complicates the determination of the exact pathophysiological roles that complement has in trauma, burn, and sepsis. Literature reporting on these three conditions is often controversial regarding the importance, distribution, and temporal occurrence of complement activation products further hampering the deduction of defined pathophysiological pathways driven by complement. Nevertheless, many in vitro experiments and animal models have shown beneficial effects of complement inhibition at different levels of the cascade. In the future, not only inhibition but also a complement reconstitution therapy should be considered in prospective studies to expedite how meaningful complement-targeted interventions need to be tailored to prevent complement augmented multi-organ failure after trauma, burn, and sepsis.This review summarizes clinically relevant studies investigating the role of complement in the acute diseases trauma, burn, and sepsis with important implications for clinical translation.
Le sertâo sisalier de Bahia-Brésil : analyse d'images spot pour une typologie dynamique de l'utilisation des terres (1986-1993) (1996)

Ce travail a pour objectif d'etablir un diagnostic du changement dans l'utilisation des terres, a partir de trois series de donnees spot teledetectees entre 1986 et 1993, periode-cle de mutation du sertao sisalier de l'etat de bahia, au coeur du nordeste semi-aride bresilien. L'equilibre relatif entre boeuf, sisal et caatinga qui existait depuis les annees 1930, s'est rompu dans les annees 1980. Conjointement au defrichement de la caatinga, on assiste a l'abandon partiel de la culture sisaliere,qu'elle soit traditionnelle ou industrielle au profit de l'espace pastoral, temoin du developpement de l'elevage extensif. Apres caracterisation des reponses radiometriques des differents modalites de couverture du sol, l'interpretation visuelle des images multitemporelles monocanal a permis de jeter les bases d'une typologie thematico-dynamique dont la representation spatiale est assuree par des classifications supervisees, operees sur l'ensemble des canaux bruts des trois images. Les principaux changements intervenus entre 1986 et 1993 sont ainsi identifies et estimes quantitativement.
Assessing Cognitive Function in Multiple Sclerosis With Digital Tools: Observational Study (Preprint) (2020)

<sec> <title>BACKGROUND</title> Cognitive impairment (CI) is one of the most prevalent symptoms of multiple sclerosis (MS). However, it is difficult to include cognitive assessment as part of MS standard care since the comprehensive neuropsychological examinations are usually time-consuming and extensive. </sec> <sec> <title>OBJECTIVE</title> To improve access to CI assessment, we evaluated the feasibility and potential assessment sensitivity of a tablet-based cognitive battery in patients with MS. </sec> <sec> <title>METHODS</title> In total, 53 participants with MS (24 [45%] with CI and 29 [55%] without CI) and 24 non-MS participants were assessed with a tablet-based cognitive battery (Adaptive Cognitive Evaluation [ACE]) and standard cognitive measures, including the Symbol Digit Modalities Test (SDMT) and the Paced Auditory Serial Addition Test (PASAT). Associations between performance in ACE and the SDMT/PASAT were explored, with group comparisons to evaluate whether ACE modules can capture group-level differences. </sec> <sec> <title>RESULTS</title> Correlations between performance in ACE and the SDMT (R=–0.57, &lt;i&gt;P&lt;/i&gt;&lt;.001), as well as PASAT (R=–0.39, &lt;i&gt;P&lt;/i&gt;=.01), were observed. Compared to non-MS and non-CI MS groups, the CI MS group showed a slower reaction time (CI MS vs non-MS: &lt;i&gt;P&lt;/i&gt;&lt;.001; CI MS vs non-CI MS: &lt;i&gt;P&lt;/i&gt;=.004) and a higher attention cost (CI MS vs non-MS: &lt;i&gt;P&lt;/i&gt;=.02; CI MS vs non-CI MS: &lt;i&gt;P&lt;/i&gt;&lt;.001). </sec> <sec> <title>CONCLUSIONS</title> These results provide preliminary evidence that ACE, a tablet-based cognitive assessment battery, provides modules that could potentially serve as a digital cognitive assessment for people with MS. </sec> <sec> <title>CLINICALTRIAL</title> ClinicalTrials.gov NCT03569618; https://clinicaltrials.gov/ct2/show/NCT03569618 </sec>
Closed-Form Theory of Kerr Frequency Combs (2015)

A closed-form particular solution is identified for Kerr frequency combs and simple scaling laws are developed. The behavior of both soliton and wavetrain waveforms are reproduced and new regimes of performance are predicted.
Supplementary Material for: MicroRNA miR-371a-3p - A Novel Serum Biomarker of Testicular Germ Cell Tumors: Evidence for Specificity from Measurements in Testicular Vein Blood and in Neoplastic Hydrocele Fluid (2016)

&lt;br&gt;&lt;strong&gt;&lt;em&gt;Background:&lt;/em&gt;&lt;/strong&gt; microRNAs (miRs)-371-3 are suggested to be novel biomarkers of germ cell tumors (GCTs), but their specificity is unresolved. We aimed at clarifying the origin of miR 371a-3p by measuring this miR in peripheral vein blood, and in fluids present in the vicinity of GCTs. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; miR-371a-3p levels were measured by quantitative PCR in 9 tumor surrounding hydroceles and in cubital vein blood (CVB) and testicular vein blood (TVB) of 64 GCT patients, 51 with clinical stage (CS) 1, 13 with CS2-3. Thirty three CS1 cases had also postoperative CVB measurement. TVB miR levels were compared with those of CVB. Associations with clinical factors were analyzed statistically. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; TVB miR levels were 294-fold, 80-fold and 4.6-fold higher than those in CVB of CS1 patients, CS2-3 patients and controls, respectively. Neoplastic hydrocele fluid comprised of very high miR levels. In CS1, miR levels dropped to normal postoperatively. Statistically, CVB miR levels are significantly associated with tumor size (p = 0.0211) and testis length (p = 0.0493). TVB miR levels are associated with testis length (p = 0.0129). &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; This study provides evidence for the origin of circulating miR 371a-3p molecules from GCT cells. miR-371a-3p represents a specific serum biomarker for germ cell cancer.
From Resistance to Receptiveness: Farmer Willingness to Participate in Extension Discussions About Climate Variability and Climate Change (2016)

Identifying what Extension professionals believe are the critical elements of a communication strategy that is most likely to encourage agricultural producers to participate in discussions of climate variability and climate change is pivotal to providing timely solutions to issues facing farmers. The current study involved interviews with 50 Extension professionals from four southeastern states (Alabama, Florida, Georgia, and South Carolina) who were engaged in ongoing work related to climate and agriculture. Respondents were asked to assess how best to engage farmers in conversations related to climate variability and climate change. Qualitative analysis showed that Extension professionals recommended avoiding content related to politics, attribution of climate change to human causes, and telling farmers what to do. Respondents recommended emphasizing adaptation strategies, climate variability over climate change, evidence that climate change exists, and the financial benefits for farmers. In addition, Extension professionals proposed several delivery methods they thought would be most effective with farmers, including delivery tailored to the characteristics of the audience, a positive overall tone, and an understanding that engagement should be viewed as a long-term process based on building relationships with farmers. The findings suggest that farmers are a potentially receptive audience on climate issues when properly approached.
Mechanical model for the generation of acoustic chaos in sonic infrared imaging (2004)

We describe a mechanical model for the generation of complex vibrations with fractional “subharmonics” from the contact between a sharply tuned ultrasonic source and a rigid object. The frequency patterns generated by the model mimic the patterns observed in samples undergoing sonic IR imaging. The output of the model is chaotic in the sense that the output appears to lack continuity with respect to the input parameters.
ChemInform Abstract: A NOVEL TETRACYCLIC RING SYSTEM. 10H‐TETRAZOLO(5′,1′:3,4)(1,2,4)TRIAZINO(5,6‐B)INDOLE (1981)

Abstract Aus den 2,3‐Indol‐dionen (I) entstehen mit Thiosemicarbazid (II) die Kondensationsprodukte (III), aus denen die Hydrazine (IV) entstehen, welche mit salpetriger Säure zu den Aziden (V) führen, die im Gleichgewicht mit (VI) vorliegen.
ChemInform Abstract: The Formation of 2‐Hydroxy‐4‐hydroxymethyl‐3‐(indol‐3‐yl)‐cyclopent‐2‐enone Derivatives from Ascorbigens. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Minimally Invasive All Arthroscopic Broström With InternalBrace Augmentation: A Technique Tip (2021)

Minimally invasive and all-arthroscopic lateral ligament repairs are increasingly popular in the ankle. These techniques are biomechanically and clinically as successful as their equivalent open procedures. Open lateral ligament repairs have benefitted by the inclusion of a suture tape to augment the strength of the repair and allow for earlier, accelerated rehabilitation. We present an arthroscopic technique to incorporate the benefits of minimally invasive ligament repair with the inclusion of the suture tape augmentation. This allows for immediate postoperative weight bearing, accelerated rehabilitation, and rapid return to function while minimizing scarring and wound complications. Level of Evidence: Diagnostic Level V, expert opinion. See Instructions for Authors for a complete description of levels of evidence.
Cytoplasmic Localization of Prostate-Specific Membrane Antigen Inhibitors May Confer Advantages for Targeted Cancer Therapies (2021)

Targeted imaging and therapy approaches based on novel prostate-specific membrane antigen (PSMA) inhibitors have fundamentally changed the treatment regimen of prostate cancer. However, the exact mechanism of PSMA inhibitor internalization has not yet been studied, and the inhibitors' subcellular fate remains elusive. Here, we investigated the intracellular distribution of peptidomimetic PSMA inhibitors and of PSMA itself by stimulated emission depletion (STED) nanoscopy, applying a novel nonstandard live cell staining protocol. Imaging analysis confirmed PSMA cluster formation at the cell surface of prostate cancer cells and clathrin-dependent endocytosis of PSMA inhibitors. Following the endosomal pathway, PSMA inhibitors accumulated in prostate cancer cells at clinically relevant time points. In contrast with PSMA itself, PSMA inhibitors were found to eventually distribute homogeneously in the cytoplasm, a molecular condition that promises benefits for treatment as cytoplasmic and in particular perinuclear enrichment of the radionuclide carriers may better facilitate the radiation-mediated damage of cancerous cells. This study is the first to reveal the subcellular fate of PSMA/PSMA inhibitor complexes at the nanoscale and aims to inspire the development of new approaches in the field of prostate cancer research, diagnostics, and therapeutics. SIGNIFICANCE: This study uses STED fluorescence microscopy to reveal the subcellular fate of PSMA/PSMA inhibitor complexes near the molecular level, providing insights of great clinical interest and suggestive of advantageous targeted therapies. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/8/2234/F1.large.jpg.
Microprocessing of glass materials by laser-induced plasma-assisted ablation using nanosecond pulsed lasers (2000)

In this paper, we demonstrate formation of micro-grating in fused silica by laser-induced plasma assisted-ablation using different wavelength lasers projected through a metallic mask. With becoming longer wavelengths from 266,532 to 1060nm, the ablation rate of fused silica at 1.5J/cm<SUP>2</SUP> decreases from 21,2 to nm/pulse. While the ablation threshold of laser fluence increases from 0.7, 1.5 to 3.75 J/cm<SUP>2</SUP>. The 2.0mm deep through holes in Pyrex glass are drilled by single-beam 532nm-laser ablation. While the same deep through holes in fused quartz are only drilled by double-pulse-train of 532nm-laser ablation with a time-delay of 3.3ns. Finally, the ablation process was analyzed by an in-situ observation of laser-produced plasma, revealing different natures for surface patterning and channel- drilling.
Comparison of GIST and LAMP on the GAW15 simulated data (2007)

After genetic linkage has been identified for a complex disease, the next step is often fine-mapping by association analysis, using single-nucleotide polymorphisms (SNPs) within a linkage region. If a SNP shows evidence of association, it is useful to know whether the linkage result can be explained in part or in full by the candidate SNP. The genotype identity-by-descent sharing test (GIST) and linkage and association modeling in pedigrees (LAMP) are two methods that were specifically proposed to address this question. GIST determines whether there is significant correlation between family-specific weights, defined by the presence of a tentatively associated allele in affected siblings, and family-specific nonparametric linkage scores. LAMP constructs a pedigree likelihood function of the marker data conditional on the trait data, and implements three likelihood ratio tests to characterize the relationship between the candidate SNP and the disease locus. The goal of our study was to compare the two approaches and evaluate their ability to identify disease-associated SNPs in the Genetic Analysis Workshop 15 (GAW15) simulated data. Our results can be summarized as follows: 1) GIST is simple and fast but, as a test of association, did not perform well in the GAW15 data, especially with adjustment for multiple testing; 2) as a test of association, the LAMP-LE test performs best when the linkage evidence is strong, or when there is at least moderate linkage disequilibrium between the candidate SNP and the trait locus. We conclude that LAMP is more flexible and reliable to use in practice.
Plasma Biomarkers of AD Emerging as Essential Tools for Drug Development: An EU/US CTAD Task Force Report (2019)

There is an urgent need to develop reliable and sensitive blood-based biomarkers of Alzheimer's disease (AD) that can be used for screening and to increase the efficiency of clinical trials. The European Union-North American Clinical Trials in Alzheimer's Disease Task Force (EU/US CTAD Task Force) discussed the current status of blood-based AD biomarker development at its 2018 annual meeting in Barcelona, Spain. Recent improvements in technologies to assess plasma levels of amyloid beta indicate that a single sample of blood could provide an accurate estimate of brain amyloid positivity. Plasma neurofilament light protein appears to provide a good marker of neurodegeneration, although not specific for AD. Plasma tau shows some promising results but weak or no correlation with CSF tau levels, which may reflect rapid clearance of tau in the bloodstream. Blood samples analyzed using -omics and other approaches are also in development and may provide important insight into disease mechanisms as well as biomarker profiles for disease prediction. To advance these technologies, international multidisciplinary, multi-stakeholder collaboration is essential.
Serum Creatinine in the Critically Ill Patient With Sepsis (2018)

Following esophageal resection for cancer, a 73-year-old man was admitted to the ICU with pneumonia and progressive acute respiratory failure, and he was placed on mechanical ventilation. At day 5, his creatinine level continued to increase. How would you proceed?
Ultrasound Cyclo Plasty for Treatment of Surgery-Naïve Open-Angle Glaucoma Patients: A Prospective, Multicenter, 2-Year Follow-Up Trial (2021)

Ultrasound Cyclo Plasty is a valuable, effective and well-tolerated procedure to lower IOP in patients with open-angle glaucoma without previous filtering surgery.