Miracle-dz/UniFAR-FTUs huggingface dataset:
Probing single-tumor cell interactions with different-age type I collagen networks by synchrotron-based Fourier transform infrared microspectroscopy

Abstract. We report here on a first study using synchrotron radiation-based Fourier transform infrared microspectroscopy and imaging to investigate HT1080 human fibrosarcoma cells grown onto different-aged type I collagen networks. Spectral images were analyzed with k-means and fuzzy C-means (FCM) clustering algorithms. K-means delineated tumor cells from their surrounding collagen networks and the latter as a function of age mainly due to specific changes in the sugar absorption region. The FCM analysis gave a better nuance of the spectral images. A progression of the biochemical information was observed upon going from the cellular compartments to the pericellular contact regions and to the intact collagens of the different age groups. Two spectral markers based on sugar and protein bands via the intensity ratio (I1032/I1655) and band area ratio (Asugar/Aamide II), showed an increase in advanced glycation endproducts (AGEs) with age. A clear-separation of the three age groups was obtained for spectra originating from the peripheral contact areas mainly due to changes in protein band intensities. The above-described markers decreased to constant levels for the three conditions indicating a masking of the biochemical information. These results hold promises to better understand the impact of age on tumor progression processes while highlighting new markers of the tumor cell invasion front.
Development of Harmaline-induced Tremor in a Swine Model

Background In the field of translational neuroscience research, it is critical to utilize a large animal model to test the feasibility, safety, and functionality of novel therapies. Here, we describe a protocol for the development of a large animal model of tremor. Methods In a pig model, tremor was induced with harmaline and measured with wireless accelerometers attached to the limbs. Three different doses of harmaline were tested and three repetitive injections were made at 72-hour intervals. To fully characterize the drug-induced tremor, onset time, tremor amplitude, maintained duration, and peak tremor frequency were analyzed. Results Harmaline-induced tremor appeared immediately following intravenous injection of harmaline. Tremor was maintained over 2 hours. Its frequency was 10–16 Hz, which was independent of doses. Dose-dependent responses were observed in tremor amplitude, triggering time, and tremor-maintained duration. Repetitive injection of harmaline desensitized the harmaline effect. Discussion We provide a detailed protocol for training, drug injection, device selection, and tremor recording optimized to create a swine model of tremor with harmaline. Our protocol provides reliable tremor in pigs and suggests pig as a valid translational large animal model of tremor.
‘Developmental Delay’ Reconsidered: The Critical Role of Age-Dependent, Co-variant Development

In memory of Annette Karmiloff-Smith. This paper reviews recent neurobiological research reporting structural co-variance and temporal dependencies in age-dependent gene expression, parameters of cortical maturation, long range connectivity and interaction of the biological network with the environment. This research suggests that age by size trajectories of brain structures relate to functional properties more than absolute sizes. In line with these findings, recent behavioral studies of typically developing children whose language development was delayed reported long term consequences of such delays. As for neurodevelopmental disorders, disrupted developmental timing and slow acquisitional pace are hallmarks of these populations. It is argued that these behavioral and neuro-biological results highlight the need to commit to a developmental model which will reflect the fact that temporal dependencies overseeing structural co-variance among developmental components are major regulatory factors of typical development of the brain/mind network. Consequently, the concept of ‘developmental delay’ in developmental theorizing needs to be reconsidered.
Effect of Ceramic Powder Particle Size Distribution on its Reactivity in Lime-Based Binders

Application of various pozzolanic materials is the current approach to obtain suitable environmental, economic and durability parameters of composites, in which they are used. Considerable interest is focused on the possibilities of finely ground ceramic powder (CP) exhibiting pozzolanic activity. Present paper is aimed at the experimental study on the monitoring of reaction kinetics in lime-ceramic powder system (1:1). Ceramic powders with controlled grading were used. Reaction capacity was assessed in time by means of thermogravimetry. The dominant effect of the finest fractions (up to 0.030 mm) on the pozzolanic reaction was proved; coarser fractions of used CP exhibited approximately the half reaction efficiency after 28 days of curing.
Gender Differences in Drinking Practices in Middle Aged and Older Russians

Aims: The study investigated gender differences in drinking patterns and the reasons behind them among men and women in the Russian city of Novosibirsk. Methods: A mixed method, combining quantitative and qualitative data, was conducted based on the Health, Alcohol and Psychosocial factors In Eastern Europe cohort study. The quantitative study included 4268 men and 5094 women aged 45–69 years; of those, 20 men and 24 women completed an in-depth interview. Results: The quantitative data revealed a large gap in drinking patterns in general between genders. Women drank less often and much smaller quantities than that of men. For example, 19% of men, vs. 1% of women, were classified as problem drinkers (two or more positive answers on the CAGE questionnaire). These differences were not explained by socioeconomic factors. Qualitative data have shown that gender roles and a traditional culture around women's and men's drinking were the main reasons for the reported drinking behaviour, whereby women were consistently expected to drink much less than men in terms of preference for strong beverages, drinking frequency and quantity of alcohol consumed. Conclusion: The study confirmed that large differences exist between Russian men's and women's drinking; these differences may be largely explained by gender roles.
Randomized trial demonstrates that extended-release epidural morphine may provide safe pain control for lumbar surgery patients

Background: Safe and effective postoperative pain control remains an issue in complex spine surgery. Spinal narcotics have been used for decades but have not become commonplace because of safety or re-dosing concerns. An extended release epidural morphine (EREM) preparation has been used successfully in obstetric, abdominal, thoracic, and extremity surgery done with epidural anesthesia. This has not been studied in open spinal surgery. Methods: Ninety-eight patients having complex posterior lumbar surgery were enrolled in a partially randomized clinical trial (PRCT) of low to moderate doses of EREM. Surgery included levels from L3 to S1 with procedures involving combinations of decompression, instrumented arthrodesis, and interbody grafting. The patients were randomized to receive either 10 or 15 mg of EREM through an epidural catheter placed under direct vision at the conclusion of surgery. Multiple safety measures were employed to prevent or detect respiratory depression. Postoperative pain scores, narcotic utilization, and adverse events were recorded. Results: There were no significant differences between the two groups as to supplemental narcotic requirements, pain scores, or adverse events. There were no cases of respiratory depression. The epidural narcotic effect persisted from 3 to 36 hours after the injection. Conclusion: By utilizing appropriate safety measures, EREM can be used safely for postoperative pain control in lumbar surgery patients. As there was no apparent advantage to the use of 15 mg, the lower 10 mg dose should be used.
Contrast media-induced nephropathy: how has Italy contributed in the past 30 years? A systematic review

Background and objective The use of contrast media in Italy has exponentially increased in the past 3 decades. However, it is unknown whether there has been an increase in clinical research evaluating the risks associated with contrast media usage, especially regarding contrast-induced nephropathy. To fill this gap in knowledge, we performed a systematic review. Study eligibility criteria Meta-analyses, observational studies, and clinical trials assessing contrast media-induced nephropathy as the safety outcome, in which at least one author was affiliated with an Italian university/health care structure, were eligble. Data sources Ovid MEDLINE, Ovid Embase, Cochrane Methodology Register, and Web of Science were screened. Participants Men and women exposed to contrast media. Results In total, 60 original articles were retrieved with an incremental trend between 1990 and 2017. Cohort studies were the most common study design represented. In total, 45 of 60 (75.0%) studies were monocenter studies and 41 of 60 (68.3%) received no funding. In all, 91.7% of studies disclosed no conflicts of interest and 81.7% had no external collaboration. Most of the studies provided a level of evidence of III-2 (32/60; 53.3%) and II (23/60; 38.3%). In total, 50 of 60 studies (83.3%) were published in a scientific journal ranked in the first quartile of their subject area. Conclusion There was an increased number of studies evaluating contrast-induced nephropathy in Italy during the last three decades. These studies covered procedures to prevent contrast-induced nephropathy or aimed to identify risk factors, biomarkers, and scores, and their related prognosis.
Roles of the Ubiquitin/Proteasome Pathway in Pollen Tube Growth with Emphasis on MG132-Induced Alterations in Ultrastructure, Cytoskeleton, and Cell Wall Components1[W]

The ubiquitin/proteasome pathway represents one of the most important proteolytic systems in eukaryotes and has been proposed as being involved in pollen tube growth, but the mechanism of this involvement is still unclear. Here, we report that proteasome inhibitors MG132 and epoxomicin significantly prevented Picea wilsonii pollen tube development and markedly altered tube morphology in a dose- and time-dependent manner, while hardly similar effects were detected when cysteine-protease inhibitor E-64 was used. Fluorogenic kinetic assays using fluorogenic substrate sLLVY-AMC confirmed MG132-induced inhibition of proteasome activity. The inhibitor-induced accumulation of ubiquitinated proteins (UbPs) was also observed using immunoblotting. Transmission electron microscopy revealed that MG132 induces endoplasmic reticulum (ER)-derived cytoplasmic vacuolization. Immunogold-labeling analysis demonstrated a significant accumulation of UbPs in degraded cytosol and dilated ER in MG132-treated pollen tubes. Fluorescence labeling with fluorescein isothiocyanate-phalloidin and β-tubulin antibody revealed that MG132 disrupts the organization of F-actin and microtubules and consequently affects cytoplasmic streaming in pollen tubes. However, tip-focused Ca2+ gradient, albeit reduced, seemingly persists after MG132 treatment. Finally, fluorescence labeling with antipectin antibodies and calcofluor indicated that MG132 treatment induces a sharp decline in pectins and cellulose. This result was confirmed by Fourier transform infrared analysis, thus demonstrating for the first time the inhibitor-induced weakening of tube walls. Taken together, these findings suggest that MG132 treatment promotes the accumulation of UbPs in pollen tubes, which induces ER-derived cytoplasmic vacuolization and depolymerization of cytoskeleton and consequently strongly affects the deposition of cell wall components, providing a mechanistic framework for the functions of proteasome in the tip growth of pollen tubes.
Enhancement of plasma resonance in a Hi-Bi D-shaped photonic crystal fiber SPR sensor

A D-shaped fiber surface plasmon resonance (SPR) sensor based on a Hi-Bi photonic crystal fiber (PCF) is investigated with finite element method. Through changing the size of the air holes beside the fiber core, it is found that the Hi-Bi structure can enhance the plasmon resonance at mid-infrared wavelength. The effect of the two fiber core side holes as well as the different gold film thickness on plasmon resonance is numerically investigated. A high and sharp loss peak is achieved, which indicates that the sensor should have high accuracy. The sensitivity of this D-shaped PCF sensor is obtained to be 8920nm/RIU in the range of 1.37 to 1.39 and the power sensitivity is 154 dB/(cm·RIU) in the range of 1.33 to 1.36. Particularly, near 1.36, with the detection limit of 0.1 nm the resolving power of the sensor is lower than 10-4 RIU with a figure of merit of 28.6.
Differential expression of Annexin 2, SPINK1, and Hsp60 predict progression of prostate cancer through bifurcated WHO Gleason score categories in African American men

Although studies have observed several markers correlate with progression of prostate cancer (PCa), no specific markers have been identified that accurately predict the progression of this disease, even in African American (AA) men who are generally at higher risk than other ethnic groups. The primary goal of this study was to explore whether three markers could predict the progression of PCa.
Effect of carbohydrate–electrolyte consumption on insulin, cortisol hormones and blood glucose after high-intensity exercise

Abstract Objective: This study aimed to examine the effect of CHO-E consumption after high-intensity exercise on insulin, cortisol hormones and blood glucose responses, which is important for performance and recovery in athletes. Methods: Sixteen volunteers, male athletes, participated into this study. Athletes were divided into two groups as experiment (CHO-E) and placebo (PLA). Blood was taken from the athletes three times as basal, post-exercise (PE) and 2 h after ingestion of supplement (PS). Results: When inter-group comparisons, insulin was significantly higher in the CHO-E group than the PLA group at the PS phase (p < .05). Cortisol significantly decreased in the CHO-E group at the PS compared to the PE (p < .05). Conclusions: Carbohydrate–electrolyte consumption after high-intensity exercise, accelerates the recovery process by providing optimal recovery, and enable the metabolism to remain in the anabolic state by preventing it from entering in the catabolic process as well as provides hormonal balance in metabolism.
An Improved Nonlocal History-Dependent Model for Gain and Noise in Avalanche Photodiodes Based on Energy Balance Equation

We present a nonlocal history-dependent model for impact ionization gain and noise in avalanche photodiodes (APDs) especially suited for staircase APDs. The model uses a simple energy balance equation to define effective electric fields valid also in the presence of band discontinuities which are then used to express the ionization coefficients. The model parameters have been calibrated against literature data for gain and noise in GaAs and Al<sub><italic>x</italic></sub>Ga<sub>1−<italic>x</italic></sub>As <inline-formula> <tex-math notation="LaTeX">$({x} = {0.2}, {0.6}, {0.8})$ </tex-math></inline-formula> p-i-n diodes. Application to the experimental data for gain and noise in heterojunction and staircase separate absorption and multiplication APDs is reported to demonstrate the ability of the model in describing complex APD structures. It is found that, in spite of conduction band discontinuities being much larger than valence band ones, hole impact ionization contributes a significant degradation of the noise metrics in GaAs/AlGaAs staircase APDs. These nontrivial insights demonstrate the usefulness of the model to steer device design and optimization.
Do Stereo Display Deficiencies Affect 3D Pointing?

Previous work has documented that limitations of current stereo display systems affect depth perception. We performed an experiment to understand if such stereo display deficiencies affect 3D pointing for targets in front of a screen and close to the user, i.e., in peri-personal space. Our experiment compares isolated movements with and without a change in visual depth for virtual targets. Results indicate that selecting targets along the depth axis is slower and has less throughput than laterally positioned targets.
Growth of Infants Born to HIV-Infected Women in Madurai, South India

Objective: To compare the growth patterns of HIV-infected and HIV-exposed, uninfected infants. Methods: Design: Prospective cohort study. Setting: Clinic of National Institute for Research in Tuberculosis, Madurai located in the Governement Rajaji Hospital (GRH) campus. Participants: Infants born to HIV-infected women in GRH, Madurai between January 2006 to October 2008. Infants were excluded if they were too ill, or had congenital abnormalities. Intervention: Baseline socio-demographic details and feeding patterns were recorded. Clinical assessment, anthropometric measurement, complete blood count, CD4 and CD8 counts and DNA PCR testing were performed. Anthropometric assessments and immunology profile were repeated once in 3 months till 24 months of age. Main outcome: Rate of change of weight and CD4% in HIV exposed and infected infants. Results: Of 76 infants enrolled, 25 were found to be HIV-infected by DNA PCR and fourteen of them died (11 before their first birthday). Weight gain in HIV-infected infants was 0.144 kg ((95% CI: -0.237, -0.051), P=0.003) less per month compared to negative infants, after adjusting for age, gender and feeding practice. Similarly, when compared to HIV negative infants, the decline in CD4 percentage was 3.1% ((95% CI: -4.735, -1.461), P<0.001) more in HIV positive infants. Changes in height, CD4 count, head circumference and haemoglobin were not associated with HIV status. Conclusion: Growth faltering occurs early in life in HIV-infected infants and its identification is important for developing appropriate treatment and nutritional management strategies. Mortality is high in the absence of early antiretroviral treatment.
On the Diachronic Stability of Irregularity in Inflectional Morphology

Many languages' inflectional morphological systems are replete with irregulars, i.e., words that do not seem to follow standard inflectional rules. In this work, we quantitatively investigate the conditions under which irregulars can survive in a language over the course of time. Using recurrent neural networks to simulate language learners, we test the diachronic relation between frequency of words and their irregularity.
Finger Movement Recognition During Ballistic Movements Using Electromyography

Individuals who perform repetitive and spontaneous movements with their fingers such as typing on a keyboard or playing instruments are susceptible to repetitive stress injuries. We denote such movements as "ballistic gestures". The most common injury due to ballistic gestures is carpal tunnel syndrome, which occurs when typing on a keyboard using an improper typing style or hand posture. It then becomes important to pro-actively analyze an individual's finger movements and recommend changes according to their habits to prevent such injuries. In this work, we present a Gaussian mixture Hidden Markov Model classification method to classify finger movement during typing activities with an accuracy above 97%. Indeed, the model maintains such accuracy across typing speeds and different individuals. Further, we show the effects that sampling rate, electrode placement, typing speed, and movement epenthesis have on classification accuracy in ballistic gestures.
Chromosome‐scale pseudomolecules refined by optical, physical and genetic maps in flax

Genomes of varying sizes have been sequenced with next-generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimeras caused by mis-scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n = 30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high-resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs (298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 new scaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome-based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super-BNG contigs (N50 of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudomolecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the annotated genes. Evidence from the chromosome-scale pseudomolecules suggests that flax has undergone palaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions or fusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.
Shape evolution and bubble formation of acoustically levitated drops

In this study, we investigated the shape evolution and bubble formation of acoustically levitated drops upon increasing the sound intensity. Here, a levitated liquid drop evolves progressively from an oblate spheroidal shape to a flattened film to a thin bowl-shaped film, eventually forming a closed bubble. Through systematic experiments, numerical simulation, and scaling analysis, we demonstrate that the buckled geometry of the liquid film can drastically enhance the suction effect of acoustic radiation pressure at its rim, forming a significant pressure gradient inside the film which causes an abrupt area expansion and bubble formation. Our results provide the mechanical origin responsible for the shape evolution and bubble formation of acoustically levitated drops, and highlight the role of buckled geometry in the levitation and manipulation of liquid films in an ultrasound field.
Breaking the Tracking: Enabling Weight Perception using Perceivable Tracking Offsets

Virtual reality (VR) technology strives to enable a highly immersive experience for the user by including a wide variety of modalities (e.g. visuals, haptics). Current VR hardware however lacks a sufficient way of communicating the perception of weight of an object, resulting in scenarios where users can not distinguish between lifting a bowling ball or a feather. We propose a solely software based approach of simulating weight in VR by deliberately using perceivable tracking offsets. These tracking offsets nudge users to lift their arm higher and result in a visual and haptic perception of weight. We conducted two user studies showing that participants intuitively associated them with the sensation of weight and accept them as part of the virtual world. We further show that compared to no weight simulation, our approach led to significantly higher levels of presence, immersion and enjoyment. Finally, we report perceptional thresholds and offset boundaries as design guidelines for practitioners.