Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogeny, systematics, and revision of the type species of Lobomonas, L. francei (Volvocales, Chlorophyta) and closely related taxa

In the present study, three new strains of the rare volvocalean green alga Lobomonas were isolated from field‐collected samples, one from Sardinia (Italy) and two from Argentina, and comparatively studied. The Sardinian and one of the Argentinian strains were identified as Lobomonas francei, the type species of the genus, whereas the second Argentinian strain corresponded to L. panduriformis. Two additional nominal species of Lobomonas from culture collections (L. rostrata and L. sphaerica) were included in the analysis and shown to be morphologically and molecularly identical to the L. francei strains. The presence, number, and shapes of cell wall lobes, the diagnostic criterion of Lobomonas, were shown to be highly variable depending on the chemical composition of the culture medium used. The analyses by SEM gave evidence that the cell wall lobes in Lobomonas originate at the junctions of adjacent cell wall plates by extrusion of gelatinous material. The four L. francei strains had identical nrRNA gene sequences and differed by only one or two substitutions in the ITS1 + ITS2 sequences. In the phylogenetic analyses, L. francei and L. panduriformis were sister taxa; however, another nominal Lobomonas species (L. monstruosa) did not belong to this genus. Lobomonas, together with taxa designated as Vitreochlamys, Tetraspora, and Paulschulzia, formed a monophyletic group that in the combined analyses was sister to the “Chlamydomonas/Volvox‐clade. ” Based on these results, Lobomonas was revised, the diagnosis of the type species emended, a lectotype and an epitype designated, and several taxa synonymized with the type species.
Studying the effects of the heat stress on the various layers of human skin using damage function

This paper develops a model to identify the effects of thermal stress on temperature distribution and damage in human dermal regions. The design and selection of the model takes into account many factors effecting the temperature distribution of skin, e.g., thermal conductance, perfusion, metabolic heat generation and thermal protective capabilities of the skin. The transient temperature distribution within the region is simulated using a two-dimensional finite element model of the Pennes’ bioheat equation. The relationship between temperature and time is integrated to view the damage caused to human skin by using Henriques’ model Henriques, F. C. , Arch. Pathol. 43 (1947) 489–502]. The Henriques’ damage model is found to be more desirable for use in predicting the threshold of thermal damage. This work can be helpful in both emergency medicines as well as to plastic surgeon in deciding upon a course of action for the treatment of different burn injuries.
A Review of Scrub Typhus (Orientia tsutsugamushi and Related Organisms): Then, Now, and Tomorrow

Scrub typhus and the rickettsial diseases represent some of the oldest recognized vector-transmitted diseases, fraught with a rich historical aspect, particularly as applied to military/wartime situations. The vectors of Orientia tsutsugamushi were once thought to be confined to an area designated as the Tsutsugamushi Triangle. However, recent reports of scrub typhus caused by Orientia species other than O. tsutsugamushi well beyond the limits of the Tsutsugamushi Triangle have triggered concerns about the worldwide presence of scrub typhus. It is not known whether the vectors of O. tsutsugamushi will be the same for the new Orientia species, and this should be a consideration during outbreak/surveillance investigations. Additionally, concerns surrounding the antibiotic resistance of O. tsutsugamushi have led to considerations for the amendment of treatment protocols, and the need for enhanced public health awareness in both the civilian and medical professional communities. In this review, we discuss the history, outbreaks, antibiotic resistance, and burgeoning genomic advances associated with one of the world’s oldest recognized vector-borne pathogens, O. tsutsugamushi.
Common Sense in Choice: The Effect of Sensory Modality on Neural Value Representations

Abstract Although it is well established that the ventromedial prefrontal cortex (vmPFC) represents value using a common currency across categories of rewards, it is unknown whether the vmPFC represents value irrespective of the sensory modality in which alternatives are presented. In the current study, male and female human subjects completed a decision-making task while their neural activity was recorded using functional magnetic resonance imaging. On each trial, subjects chose between a safe alternative and a lottery, which was presented visually or aurally. A univariate conjunction analysis revealed that the anterior portion of the vmPFC tracks subjective value (SV) irrespective of the sensory modality. Using a novel cross-modality multivariate classifier, we were able to decode auditory value based on visual trials and vice versa. In addition, we found that the visual and auditory sensory cortices, which were identified using functional localizers, are also sensitive to the value of stimuli, albeit in a modality-specific manner. Whereas both primary and higher-order auditory cortices represented auditory SV (aSV), only a higher-order visual area represented visual SV (vSV). These findings expand our understanding of the common currency network of the brain and shed a new light on the interplay between sensory and value information processing.
Early detection and intervention in psychosis: an ethical paradigm shift

Summary This paper will first posit the rationale for intervention before onset, then outline the current usual practice of treating schizophrenia and the determinants ofthat practice. Recent developments that permit or demand a change in this practice will then be elaborated. The article concludes with an elaboration of the currently known risks and benefits of early intervention research. The ethics of early intervention are undergoing a paradigm shift, a shift that supports early intervention research as being necessary to bring empirical balance to territory that is currently overpopulated with zealous opinions. Delcaration of interest None.
Comparison of survival between lung cancer patients receiving single or multiple-incision thoracoscopic surgery.

Background The effect of single-incision thoracoscopic surgery for lung cancer on long-term survival is unknown and no studies have investigated whether there are differences in survival between single and multiple incision approaches. We aimed to compare long-term overall survival and disease-free survival of patients who underwent single-incision thoracoscopic surgery with those who received multiple-incision thoracoscopic surgery for lung cancer. Methods We retrospectively analyzed 532 patients with lung cancer who underwent either single-incision (n=150) or multiple-incision thoracoscopic resection (n=382) during the period January 2000 to December 2014. Patients were matched on propensity score at a 1:2 ratio to estimate the effect of treatment on long-term and disease-free survival. Overall survival and disease-free survival were assessed using the Kaplan-Meier method, the log-rank test and Cox proportional-hazards regression. Results Propensity matching resulted in 138 patients in the single-incision group and 276 patients in the multiple-incision group. The matched patients in the single-incision group had a significantly better 5-year overall survival than those in the multiple-incision group (P=0.027). Disease-free survival was similar between the two groups before and after matching. The number of chest wall incisions did not influence overall survival or disease-free survival. Conclusions The long-term outcomes of single-incision thoracoscopic surgery are comparable to those of multiple-incision thoracoscopic surgery for lung cancer.
Considerations for optimization of microRNA PCR assays for molecular diagnosis

ABSTRACT The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The heterogeneity of microRNAs, with each one comprising a series of variants or ‘isomiRs’, adds additional complexity. Presented here are the key considerations for use of RT-qPCR to measure microRNAs and their isomiRs, with a focus on plasma. Modified nucleotides can be incorporated into primer sequences to enhance affinity and provide increased specificity and sensitivity for RT-qPCR assays. Approaches based upon polyA tailing and use of a common oligo(dT)-based reverse transcription oligonucleotide will detect most isomiRs. Conversely, stem-loop RT oligonucleotides and sequence specific probes can enable detection of specific isomiRs of interest. Next generation sequencing of all the products of a microRNA RT-PCR reaction is a promising new approach for both microRNA quantification and characterization.
Biomarker and Clinical Trial Design Support for Disease-Modifying Therapies: Report of a Survey of the EU/US: Alzheimer’s Disease Task Force

BackgroundDisease-modifying therapies are urgently needed for the treatment of Alzheimer’s disease (AD). The European Union/United States (EU/US) Task Force represents a broad range of stakeholders including biopharma industry personnel, academicians, and regulatory authorities.ObjectivesThe EU/US Task Force represents a community of knowledgeable individuals who can inform views of evidence supporting disease modification and the development of disease-modifying therapies (DMTs). We queried their attitudes toward clinical trial design and biomarkers in support of DMTs.Design/Setting/ParticiantsA survey of members of the EU/US Alzheimer’s Disease Task Force was conducted. Ninety-three members (87%) responded. The details were analyzed to understand what clinical trial design and biomarker data support disease modification.Measurements/Results/ConclusionsTask Force members favored the parallel group design compared to delayed start or staggered withdrawal clinical trial designs to support disease modification. Amyloid biomarkers were regarded as providing mild support for disease modification while tau biomarkers were regarded as providing moderate support. Combinations of biomarkers, particularly combinations of tau and neurodegeneration, were regarded as providing moderate to marked support for disease modification and combinations of all three classes of biomarkers were regarded by a majority as providing marked support for disease modification. Task Force members considered that evidence derived from clinical trials and biomarkers supports clinical meaningfulness of an intervention, and when combined with a single clinical trial outcome, nearly all regarded the clinical trial design or biomarker evidence as supportive of disease modification. A minority considered biomarker evidence by itself as indicative of disease modification in prevention trials. Levels of evidence (A,B,C) were constructed based on these observations.ConclusionThe survey indicates the view of knowledgeable stakeholders regarding evidence derived from clinical trial design and biomarkers in support of disease modification. Results of this survey can assist in designing clinical trials of DMTs.
COMMENTARY The utility of transcriptomics in fish conservation

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
Detection of atrial fibrillation using an earlobe photoplethysmographic sensor

Atrial fibrillation (AF) is the most common cardiac arrhythmia in the world, associated with increased risk of thromboembolic events and an increased mortality rate. In addition, a significant portion of AF patients are asymptomatic. Current AF diagnostic methods, often including a body surface electrocardiogram or implantable loop recorder, are both expensive and invasive and offer limited access within the general community. Objective: We tested the feasibility of the detection of AF using a photoplethysmographic signal acquired from an inexpensive, non-invasive earlobe photoplethysmographic sensor. This technology can be implemented into wearable devices and would enable continuous cardiac monitoring capabilities, greatly improving the rate of asymptomatic AF detection. Approach: We conducted a clinical study of patients going through electrical cardioversion for AF treatment. Photoplethysmographic recordings were taken from these AF patients before and after their cardioversion procedure, along with recordings from a healthy control group. Using these recordings, cardiac beats were identified and the inter-systolic interval was calculated. The inter-systolic interval was used to calculate four parameters to quantify the heart rate variability indicative of AF. Receiver operating characteristic curves were used to calculate discriminant thresholds between the AF and non-AF cohorts. Main results: The parameter with the greatest discriminant capability resulted in a sensitivity and specificity of 90.9%. These results are comparable to expensive ECG-based and invasive implantable loop recorder AF detection methods. Significance: These results demonstrate that using a non-invasive earlobe photoplethysmographic signal is a viable and inexpensive alternative to ECG-based AF detection methods, and an alternative that could be invaluable in detecting subclinical AF.
Implicit Coordination of Caches in Small Cell Networks Under Unknown Popularity Profiles

We focus on a dense cellular network, in which a limited-size cache is available at every base station (BS). In order to optimize the overall performance of the system in such scenario, where a significant fraction of the users is covered by several BSs, a tight coordination among nearby caches is needed. To this end, this paper introduces a class of simple and fully distributed caching policies, which require neither direct communication among BSs nor a priori knowledge of content popularity. Furthermore, we propose a novel approximate analytical methodology to assess the performance of interacting caches under such policies. Our approach builds upon the well-known characteristic time approximation [1] and provides predictions that are surprisingly accurate (hardly distinguishable from the simulations) in most of the scenarios. Both synthetic and trace-driven results show that our caching policies achieve an excellent performance (in some cases provably optimal). They outperform state-of-the-art dynamic policies for interacting caches, and, in some cases, also the greedy content placement, which is known to be the best performing polynomial algorithm under static and perfectly known content popularity profiles.
A Improved Structure for Substrate Integrated Waveguide Composite Right/Left-handed Cell

The composite right/left-handed (CRLH) transmission line (TL) based leaky-wave antennas (LWAs) are usually constrained by wide frequency scanning bandwidths to achieve certain beam scanning range. This is mainly due to that the fast wave region of the CRLH cell dispersion is insensitive to the frequency. In this work, we propose a substrate integrated waveguide (SIW) CRLH cell structure with dispersion sensitivity improved. This advantage makes the structure have a narrower fast wave region and thus have a potential application to the LWA with a large beam scanning range (BSR)/bandwidth ratio. The simulated and experimental results of this CRLH unit cell are both given to confirm the validity of the dispersion sensitivity promotion.
A fluorophore ligase for site-specific protein labeling inside living cells

Biological microscopy would benefit from smaller alternatives to green fluorescent protein for imaging specific proteins in living cells. Here we introduce PRIME (PRobe Incorporation Mediated by Enzymes), a method for fluorescent labeling of peptide-fused recombinant proteins in living cells with high specificity. PRIME uses an engineered fluorophore ligase, which is derived from the natural Escherichia coli enzyme lipoic acid ligase (LplA). Through structure-guided mutagenesis, we created a mutant ligase capable of recognizing a 7-hydroxycoumarin substrate and catalyzing its covalent conjugation to a transposable 13-amino acid peptide called LAP (LplA Acceptor Peptide). We showed that this fluorophore ligation occurs in cells in 10 min and that it is highly specific for LAP fusion proteins over all endogenous mammalian proteins. By genetically targeting the PRIME ligase to specific subcellular compartments, we were able to selectively label spatially distinct subsets of proteins, such as the surface pool of neurexin and the nuclear pool of actin.
High-Speed Autonomous Quadrotor Navigation through Image Paths

This paper addresses the problem of autonomous quadrotor navigation within indoor spaces. In particular, we focus on the case where a visual map of the area, represented as a graph of linked images, is constructed offline (from visual and inertial data collected beforehand) and used to determine visual paths for the quadrotor to follow. Moreover, during the actual navigation, the quadrotor employs both the 3+1pt and the 1+1pt RANSAC to efficiently determine its desired motion towards the next reference image, for both cases of sufficient and insufficient baseline (e.g., rotations in place). Lastly, we introduce an adaptive optical-flow algorithm that can accurately estimate the quadrotor’s horizontal velocity under adverse conditions (e.g., when flying over dark, textureless floors) by progressively using information from more parts of the images. The speed and robustness of our algorithms are evaluated experimentally on a commercial quadrotor navigating in the presence of dynamic obstacles (i.e., people walking), along lengthy corridors, and through tight corners, as well as across building floors via poorly-lit staircases.
Predicting diabetes mellitus using SMOTE and ensemble machine learning approach: The Henry Ford ExercIse Testing (FIT) project

Machine learning is becoming a popular and important approach in the field of medical research. In this study, we investigate the relative performance of various machine learning methods such as Decision Tree, Naïve Bayes, Logistic Regression, Logistic Model Tree and Random Forests for predicting incident diabetes using medical records of cardiorespiratory fitness. In addition, we apply different techniques to uncover potential predictors of diabetes. This FIT project study used data of 32,555 patients who are free of any known coronary artery disease or heart failure who underwent clinician-referred exercise treadmill stress testing at Henry Ford Health Systems between 1991 and 2009 and had a complete 5-year follow-up. At the completion of the fifth year, 5,099 of those patients have developed diabetes. The dataset contained 62 attributes classified into four categories: demographic characteristics, disease history, medication use history, and stress test vital signs. We developed an Ensembling-based predictive model using 13 attributes that were selected based on their clinical importance, Multiple Linear Regression, and Information Gain Ranking methods. The negative effect of the imbalance class of the constructed model was handled by Synthetic Minority Oversampling Technique (SMOTE). The overall performance of the predictive model classifier was improved by the Ensemble machine learning approach using the Vote method with three Decision Trees (Naïve Bayes Tree, Random Forest, and Logistic Model Tree) and achieved high accuracy of prediction (AUC = 0.92). The study shows the potential of ensembling and SMOTE approaches for predicting incident diabetes using cardiorespiratory fitness data.
Drug-Free Long-Term Remission in Severe Behc et ’ s Disease Following Withdrawal of Successful Anti – Tumor Necrosis Factor Treatment

Objective. To test the hypothesis that remission of Behc et’s disease (BD) in patients with severe vital organ involvement is maintained after withdrawal of successful anti–tumor necrosis factor (anti-TNF) treatment. Methods. This single-center, retrospective, longitudinal outcomes study focused on consecutive patients with disease refractory to treatment with conventional immunosuppressant agents who responded to add-on long-term anti-TNF treatment that was subsequently discontinued. The end point was the proportion of patients remaining in complete remission for at least 3 years after withdrawal of anti-TNF treatment. Results. In our BD cohort comprising 87 patients, 29 were eligible for analysis. All of these patients had disease that was refractory to conventional immunosuppressive therapy and had received successful anti-TNF treatment for a median of 2 years (interquartile range [IQR] 1.1–2.0) before treatment discontinuation. Of these patients, 12 (41%) achieved the study end point. The remaining 17 patients experienced a relapse within 1 year (IQR 0.6–1.5) after discontinuation. Re-treatment with anti-TNF was safe and effective in 14 (82%) of 17 patients; so far, 4 of these patients also achieved the study end point. Overall, 16 patients have remained in complete remission (median 6.5 years [IQR 5.5–8]). Ten of these patients are in drug-free remission (treated with anti-TNF agents, mainly for sight-threatening disease), and 6 are in azathioprine-maintained remission (treated with anti-TNF agents for ocular, intestinal, or central nervous system involvement). Notably, patients in drugfree remission were significantly younger and had a significantly shorter duration of BD when anti-TNF treatment was initiated compared to patients receiving azathioprine maintenance treatment. Conclusion. Drug-free, long-term remission after withdrawal of successful anti-TNF treatment is feasible in patients with severe BD. Because an anti-TNF agent– induced “cure” cannot be differentiated from spontaneous remission by natural history, prospective studies should examine whether anti-TNF agents should be used as first-line treatment for the induction of remission in every patient with vital organ involvement.