Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental evidence of vortex-induced vibrations at subcritical Reynolds numbers

Abstract Shedding of vortices can be observed in the wake of a fixed cylinder at Reynolds numbers larger than $Re=47$. This might give the impression that a vortex-induced vibration (VIV), which occurs when the frequency of vortex shedding in the wake of a flexibly mounted cylinder synchronizes with the natural frequency of the structure, could be observed only at Reynolds numbers larger than $Re=47$. Recent numerical simulations and theoretical work, however, have shown that it is possible to observe VIV at subcritical Reynolds numbers, i.e. Reynolds numbers smaller than $Re=47$. In these studies, a VIV has been observed numerically at Reynolds numbers as low as $Re=22$. In the present work, the first experimental evidence of VIV at subcritical Reynolds number is presented. We have designed and built an experimental set-up that makes it possible to conduct VIV experiments at subcritical Reynolds numbers, and at a constant Reynolds number over the entire lock-in range (i.e. the range for which oscillations are observed). Using this experimental set-up, we have confirmed experimentally that VIV can indeed be observed at subcritical Reynolds numbers, by observing VIV at Reynolds numbers as low as $Re=19$. We have observed subcritical VIV both when the Reynolds number stays constant over the entire lock-in range, and when the Reynolds number increases with increasing reduced velocity, while staying within the subcritical range.
Long-Term Cardiac Safety and Survival Outcomes of Neoadjuvant Pegylated Liposomal Doxorubicin in Elderly Patients or Prone to Cardiotoxicity and Triple Negative Breast Cancer. Final Results of the Multicentre Phase II CAPRICE Study

Background The CAPRICE trial was designed to specifically evaluate neoadjuvant pegylated liposomal doxorubicin (PLD) in elderly patients or in those with other cardiovascular risk factors in whom conventional doxorubicin was contraindicated. The primary analysis of the study showed a pathological complete response (pCR) of 32% and no significant decreases in LVEF during chemotherapy. Here, we report important secondary study objectives: 5-year cardiac safety, disease-free survival (DFS), overall survival (OS) and breast cancer specific survival (BCSS). Methods In this multicentre, single-arm, phase II trial, elderly patients or those prone to cardiotoxicity and high risk stage II-IIIB breast cancer received PLD (35 mg/m2) plus cyclophosphamide (600 mg/m2) every 4 weeks for 4 cycles, followed by paclitaxel for 12 weeks as neoadjuvant chemotherapy (NAC). Left ventricular ejection fraction (LVEF) monitorization, electrocardiograms and cardiac questionnaires were performed at baseline, during treatment and at 9, 16, 28 and 40 weeks thereafter. The primary endpoint was pCR and 5-year cardiac safety, DFS, BCSS and OS were also analyzed. Results Between Oct 2007, and Jun 2010, 50 eligible patients were included. Median age was 73 (35-84) years, 84% were older than 65; 64% of patients suffered from hypertension, and 10% had prior cardiac disease. Most of tumors (88%) were triple negative. No significant decreases in LVEF were observed. The mean baseline LVEF was 66.6% (52-86) and after a median follow-up of 5 years, mean LVEF was 66 (54.5-73). For intention to treat population, 5-year DFS was 50% (95% CI 40.2-68.1) and 5-year OS was 56% (95%CI 41.2-68.4). There were 8 non-cancer related deaths, achieving a 5 years BCSS of 67.74% (CI 95%:54.31%- 81.18%). Conclusion At 5-year follow-up, this PLD-based NAC regimen continued to be cardiac-safe and effective in a population of very high-risk breast cancer patients. This scheme should be considered as an option in elderly patients or in those with other risks of developing cardiotoxicity. Trial Registration Number ClinicalTrials.gov reference NCT00563953.
The COM-Poisson Process for Stochastic Modeling of Osmotic Inactivation Dynamics of Listeria monocytogenes

Controlling harmful microorganisms, such as Listeria monocytogenes, can require reliable inactivation steps, including those providing conditions (e.g., using high salt content) in which the pathogen could be progressively inactivated. Exposure to osmotic stress could result, however, in variation in the number of survivors, which needs to be carefully considered through appropriate dispersion measures for its impact on intervention practices. Variation in the experimental observations is due to uncertainty and biological variability in the microbial response. The Poisson distribution is suitable for modeling the variation of equi-dispersed count data when the naturally occurring randomness in bacterial numbers it is assumed. However, violation of equi-dispersion is quite often evident, leading to over-dispersion, i.e., non-randomness. This article proposes a statistical modeling approach for describing variation in osmotic inactivation of L. monocytogenes Scott A at different initial cell levels. The change of survivors over inactivation time was described as an exponential function in both the Poisson and in the Conway-Maxwell Poisson (COM-Poisson) processes, with the latter dealing with over-dispersion through a dispersion parameter. This parameter was modeled to describe the occurrence of non-randomness in the population distribution, even the one emerging with the osmotic treatment. The results revealed that the contribution of randomness to the total variance was dominant only on the lower-count survivors, while at higher counts the non-randomness contribution to the variance was shown to increase the total variance above the Poisson distribution. When the inactivation model was compared with random numbers generated in computer simulation, a good concordance between the experimental and the modeled data was obtained in the COM-Poisson process.
Associations Between Genotype and Peripheral Complement Proteins in First-Episode Psychosis: Evidences From C3 and C4

Schizophrenia is a common neuropsychiatric disorder with complex pathophysiology. Recent reports suggested that complement system alterations contributed to pathological synapse elimination that was associated with psychiatric symptoms in schizophrenia. Complement component 3 (C3) and complement component 4 (C4) play central roles in complement cascades. In this study, we compared peripheral C3 and C4 protein levels between first-episode psychosis (FEP) and healthy control (HC). Then we explored whether single nucleotide polymorphisms (SNPs) at C3 or C4 genes affect peripheral C3 or C4 protein levels. In total, 181 FEPs and 204 HCs were recruited after providing written informed consent. We measured serum C3 and C4 protein levels using turbidimetric inhibition immunoassay and genotyped C3 and C4 polymorphisms using the Sequenom MassArray genotyping. Our results showed that three SNPs were nominally associated with schizophrenia (rs11569562/C3: A > G, p = 0.048; rs2277983/C3: A > G, p = 0.040; rs149898426/C4: G > A, p = 0.012); one haplotype was nominally associated with schizophrenia, constructed by rs11569562–rs2277983–rs1389623 (GGG, p = 0.048); FEP had higher serum C3 and C4 (both p < 0.001) levels than HC; rs1389623 polymorphisms were associated with elevated C3 levels in our meta-analysis (standard mean difference, 0.50; 95% confidence interval, 0.30 to 0.71); the FEP with CG genotype of rs149898426 had higher C4 levels than that with GG genotypes (p = 0.005). Overall, these findings indicated that complement system altered in FEP and rs149898426 of C4 gene represented a genetic risk marker for schizophrenia likely through mediating complement system. Further studies with larger sample sizes needs to be validated.
Dynamic apico-basal enrichment of the F-actin during cytokinesis in Arabidopsis cells embedded in their tissues

Abstract Abstract Cell division is a tightly regulated mechanism, notably in tissues where malfunctions can lead to tumour formation or developmental defects. This is particularly true in land plants, where cells cannot relocate and therefore cytokinesis determines tissue topology. In plants, cell division is executed in radically different manners than in animals, with the appearance of new structures and the disappearance of ancestral mechanisms. Whilst F-actin and microtubules closely co-exist, recent studies mainly focused on the involvement of microtubules in this key process. Here, we used a root tracking system to image the spatio-temporal dynamics of both F-actin reporters and cell division markers in dividing cells embedded in their tissues. In addition to the F-actin accumulation at the phragmoplast, we observed and quantified a dynamic apico-basal enrichment of F-actin from the prophase/metaphase transition until the end of the cytokinesis.
β-Adrenergic Stimulation Synchronizes a Broad Spectrum of Action Potential Firing Rates of Cardiac Pacemaker Cells toward a Higher Population Average

The heartbeat is initiated by pacemaker cells residing in the sinoatrial node (SAN). SAN cells generate spontaneous action potentials (APs), i.e. normal automaticity. The sympathetic nervous system increases heart rate commensurate with cardiac output demand via stimulation of SAN β-adrenergic receptors (βAR). While SAN cells reportedly represent a highly heterogeneous cell population, the current dogma is that in response to βAR stimulation all cells increase their spontaneous AP firing rate in a similar fashion. The aim of the present study was to investigate cell-to-cell variability in the responses of a large population of SAN cells. We measured βAR responses among 166 single SAN cells isolated from 33 guinea pig hearts. In contrast to the current dogma, the SAN cell responses to βAR stimulation substantially varied. In each cell, changes in AP cycle length highly correlated (R2=0.97) with the AP cycle length before βAR stimulation. While, as expected, on average the cells increased their pacemaker rate, greater responses were observed in cells with slower basal rates, and vice versa, cells with higher basal rates showed smaller responses, no responses, or even decreased their rate. Thus, βAR stimulation synchronizes the operation of the SAN cell population towards a higher average rate, rather than uniformly shifting the rate in each cell, creating a new paradigm of βAR-driven fight-or-flight response among individual pacemaker cells.
Mapping the Integration of Sensory Information across Fingers in Human Sensorimotor Cortex

The integration of somatosensory signals across fingers is essential for dexterous object manipulation. Previous experiments suggest that this integration occurs in neural populations in the primary somatosensory cortex (S1). However, the integration process has not been fully characterized, as previous studies have mainly used 2-finger stimulation paradigms. Here, we addressed this gap by stimulating all 31 single- and multifinger combinations. We measured population-wide activity patterns evoked during finger stimulation in human S1 and primary motor cortex (M1) using 7T fMRI in female and male participants. Using multivariate fMRI analyses, we found clear evidence of unique nonlinear interactions between fingers. In Brodmann area (BA) 3b, interactions predominantly occurred between pairs of neighboring fingers. In BA 2, however, we found equally strong interactions between spatially distant fingers, as well as interactions between finger triplets and quadruplets. We additionally observed strong interactions in the hand area of M1. In both M1 and S1, these nonlinear interactions did not reflect a general suppression of overall activity, suggesting instead that the interactions we observed reflect rich, nonlinear integration of sensory inputs from the fingers. We suggest that this nonlinear finger integration allows for a highly flexible mapping from finger sensory inputs to motor responses that facilitates dexterous object manipulation. SIGNIFICANCE STATEMENT Processing of somatosensory information in primary somatosensory cortex (S1) is essential for dexterous object manipulation. To successfully handle an object, the sensorimotor system needs to detect complex patterns of haptic information, which requires the nonlinear integration of sensory inputs across multiple fingers. Using multivariate fMRI analyses, we characterized brain activity patterns evoked by stimulating all single- and multifinger combinations. We report that progressively stronger multifinger interactions emerge in posterior S1 and in the primary motor cortex (M1), with interactions arising between inputs from neighboring and spatially distant fingers. Our results suggest that S1 and M1 provide the neural substrate necessary to support a flexible mapping from sensory inputs to motor responses of the hand.
Mapping circuit dynamics during function and dysfunction

Neural circuits can generate many spike patterns, but only some are functional. The study of how circuits generate and maintain functional dynamics is hindered by a poverty of description of circuit dynamics across functional and dysfunctional states. For example, although the regular oscillation of a central pattern generator is well characterized by its frequency and the phase relationships between its neurons, these metrics are ineffective descriptors of the irregular and aperiodic dynamics that circuits can generate under perturbation or in disease states. By recording the circuit dynamics of the well-studied pyloric circuit in C. borealis, we used statistical features of spike times from neurons in the circuit to visualize the spike patterns generated by this circuit under a variety of conditions. This unsupervised approach captures both the variability of functional rhythms and the diversity of atypical dynamics in a single map. Clusters in the map identify qualitatively different spike patterns hinting at different dynamical states in the circuit. State probability and the statistics of the transitions between states varied with environmental perturbations, removal of descending neuromodulation, and the addition of exogenous neuromodulators. This analysis reveals strong mechanistically interpretable links between complex changes in the collective behavior of a neural circuit and specific experimental manipulations, and can constrain hypotheses of how circuits generate functional dynamics despite variability in circuit architecture and environmental perturbations.
A single full-length VAR2CSA ectodomain variant purifies broadly neutralizing antibodies against placental malaria isolates

Placental malaria (PM) is a deadly syndrome most frequent and severe in first pregnancies. PM results from accumulation of Plasmodium falciparum (Pf)-infected erythrocytes (IE) that express the surface antigen VAR2CSA and bind to chondroitin sulfate A (CSA) in the placenta. Women become PM-resistant over successive pregnancies as they develop anti-adhesion and anti-VAR2CSA antibodies, supporting VAR2CSA as the leading PM-vaccine candidate. However, the first VAR2CSA subunit vaccines failed to induce broadly neutralizing antibody and it is still unclear whether naturally acquired protective antibodies target variant or conserved epitopes. This is crucial to determine whether effective vaccines will require incorporation of many or only a single VAR2CSA allele. Here, IgG from multigravidae was sequentially purified on five full-length VAR2CSA ectodomain variants, thereby depleting IgG reactivity to each. The five VAR2CSA variants purified ∼0.7% of total IgG and yielded both strain-transcending and strain-specific reactivity to VAR2CSA and IE-surface antigen. IgG purified on the first VAR2CSA antigen displayed broad cross-reactivity to both recombinant and native VAR2CSA variants, and inhibited binding of all isolates to CSA. IgG remaining after depletion on all variants showed significantly reduced binding-inhibition activity compared to initial total IgG. These findings demonstrate that a single VAR2CSA ectodomain variant displays neutralizing epitopes shared by multiple parasites, including maternal isolates, and suggest that a broadly effective PM-vaccine can be achieved with a limited number of VAR2CSA variants.
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes

Significance Genomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Microchromosomes are gene-rich and highly conserved among birds and reptiles and share homology with one or more of the tiny chromosomes of an invertebrate that diverged from the vertebrate lineage 684 Ma. Microchromosomes interact strongly and crowd together at the center of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes, and lizards as they have fused with each other or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals. Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly, de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early-branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently, multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus, microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles and birds, that are atypical.
Quantifying phase separation property of chromatin associated proteins under physiological conditions using anti-1,6-hexanediol index

Background Liquid–liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, quantitative and global analysis of chromatin LLPS property remains absent. Results Here, by combing chromatin associated protein pull-down, quantitative proteomics and 1,6-hexanediol treatment, we developed Hi-MS and defined anti-1,6-HD index of chromatin-associated proteins (AICAP) to quantitative measurement of LLPS property of chromatin-associated proteins in their endogenous state and physiological abundance. The AICAP values were verified by previously reported experiments and were reproducible across different MS platforms. Moreover, the AICAP values were highly correlate with protein functions. Proteins act in active/regulatory biological process often exhibit low AICAP values, while proteins act in structural and repressed biological process often exhibit high AICAP values. We further revealed that chromatin organization changes more in compartment A than B, and the changes in chromatin organization at various levels, including compartments, TADs and loops are highly correlated to the LLPS properties of their neighbor nuclear condensates. Conclusions Our work provided the first global quantitative measurement of LLPS properties of chromatin-associated proteins and higher-order chromatin structure, and demonstrate that the active/regulatory chromatin components, both protein (trans) and DNA (cis), exhibit more hydrophobicity-dependent LLPS properties than the repressed/structural chromatin components.
Modified Arcsine Law for One-Bit Sampled Stationary Signals with Time-Varying Thresholds

One-bit quantization has attracted considerable attention in signal processing for communications and sensing. The arcsine law is a useful relation often used to estimate the normalized covariance matrix of zero-mean stationary input signals when they are sampled by one-bit analog-to-digital converters (ADCs)—practically comparing the signals with a given threshold level. This relation, however, only considers a zero threshold which can cause a remarkable information loss. For the first time in the literature, this paper introduces an approach to extending the arcsine law to the case where one-bit ADCs apply time-varying thresholds. In particular, the proposed method is shown to accurately recover the variance and autocorrelation of the stationary signals of interest.
Social Networking Site Use Resumption: A Model of Return Migration

This research explains why individuals resume using social networking sites (SNSs) after terminating their use. Drawing on return migration theory, we developed a theory-driven model of SNS resumption that includes two novel antecedents of SNS resumption behavior: nonuse-related dissatisfaction and use-related satisfaction. We also hypothesize that dispositional resistance to change moderates the impact of nonuse-related dissatisfaction and use-related satisfaction on resumption. We used a mixed methods approach to refine and evaluate the research model. Study 1 used the critical incident method to identify SNS-specific antecedents of nonuse-related satisfaction and use-related satisfaction, allowing us to refine the research model. Study 2 used structural equation modeling to evaluate our research model using two three-wave surveys: one with recent ex-users who recently decided to stop using and delete their profiles on Facebook and one with long-standing ex-users who stopped using and deleted their profiles on Facebook a long time ago. We found support for most relationships in our model: nonuse-related dissatisfaction and use-related satisfaction drive resumption intentions, and dispositional resistance moderates these relationships. Furthermore, we found that the time elapsed since users discontinued Facebook moderated these relationships such that the effect of nonuse-related dissatisfaction on resumption intention is stronger for recent ex-users and the effect of use-related satisfaction is stronger for long-standing ex-users. Our findings advance the understanding of resumption, an understudied behavior of the IT lifecycle and IT use and acceptance research.