Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of pamidronate administration on tooth eruption and mandibular growth in new born rats

Purpose: Bisphosphonates are commonly used drugs in pediatric patients in the treatment of osteoporotic diseases and various types of cancers. The purpose of this study was to evaluate the effects of pamidronate administration on mandibular growth and tooth eruption in new born rats. Materials and Methods: Forty Sprague Dawley rats were included in the study and divided into four groups as; 14th day pamidronate group, 30th day pamidronate group, 14th day control group and 30th day control group. Pamidronate groups were daily injected with 1.25 µg/g pamidronate disodium subcutaneously whereas control groups were injected with sterile saline. Eruption levels of lower incisor and molar teeth were assessed macroscopically. Mandibular growth was assessed by measuring reference points in cone beam tomography. Histological and histomorphometric examinations were performed under light microscope to evaluate tooth morphology and number of osteoclasts. Results: Retardation in mandibular growth, decrease in number of osteoclasts, delay in tooth eruption, degeneration in both tooth morphology and structure were observed in the pamidronate groups compared to control groups. Conclusion: Pamidronate administration during growth and development stage may adversely affect tooth eruption and mandibular growth in new born rats.
A generalized compressed sensing approach to high angular resolution diffusion imaging

Among the existing methods of diffusion MRI, high angular resolution diffusion imaging (HARDI) excels in its ability to resolve the complex orientations of crossing and branching neural fibre tracts in the brain. Unfortunately, a widespread integration of HARDI into clinical workflows is still hindered by a few practical obstacles, chief among which relates to prohibitively long scan times required by current implementations of this protocol. In addition, the dependency of HARDI on rapid acquisition schemes, such as single-shot echo planar imaging, imposes limitations on the maximal spatial resolution that one can attain at an acceptable level of signal-to-noise ratio. A possible solution to the problem of limited spatial resolution of HARDI could be to modify the pattern of k-space encoding so as to maximally utilize the bandwidth efficiency of frequency encoding at the expense of using a smaller number of phase encoding steps. At the same time, a substantial reduction in the total acquisition time could be achieved through a subcritical sampling in the q-space. Although both the above mechanisms are bound to yield highly incomplete data, a stable and reliable reconstruction of the associated HARDI signals is still possible to achieve within the framework of compressed sensing. To solve this problem, we introduce an efficient reconstruction procedure, whose effectiveness is demonstrated through both in silico and in vivo experiments.
The Distinction between Tapping and Circle Drawing with and without Tactile Feedback: An Examination of the Sources of Timing Variance

An internal clock-like process has been implicated in the control of rhythmic movements performed for short (250–2,000 ms) time scales. However, in the past decade, it has been claimed that a clock-like central timing mechanism is not required for smooth cyclical movements. The distinguishing characteristic delineating clock-like (event) from non-clock-like (emergent) timing is thought to be the kinematic differences between tapping (discrete-like) and circle drawing (smooth). In the archetypal event-timed task (tapping), presence of perceptual events is confounded with the discrete kinematics of movement (table contact). Recently, it has been suggested that discrete perceptual events help participants synchronize with a metronome. However, whether discrete tactile events directly elicit event timing has yet to be determined. In the present study, we examined whether a tactile event inserted into the circle drawing timing task could elicit event timing in a self-paced (continuation) timing task. For a majority of participants, inserting an event into the circle drawing task elicited timing behaviour consistent with the idea that an internal timekeeper was employed (a correlation of circle drawing with tapping). Additionally, some participants exhibited characteristics of event timing in the typically emergently timed circle drawing task. We conclude that the use of event timing can be influenced by the insertion of perceptual events, and it also exhibits persistence over time and over tasks within certain individuals.
The RootChip: An Integrated Microfluidic Chip for Plant Science[W][OA]

Studying development and physiology of growing roots is challenging due to limitations regarding cellular and subcellular analysis under controlled environmental conditions. We describe a microfluidic chip platform, called RootChip, that integrates live-cell imaging of growth and metabolism of Arabidopsis thaliana roots with rapid modulation of environmental conditions. The RootChip has separate chambers for individual regulation of the microenvironment of multiple roots from multiple seedlings in parallel. We demonstrate the utility of The RootChip by monitoring time-resolved growth and cytosolic sugar levels at subcellular resolution in plants by a genetically encoded fluorescence sensor for glucose and galactose. The RootChip can be modified for use with roots from other plant species by adapting the chamber geometry and facilitates the systematic analysis of root growth and metabolism from multiple seedlings, paving the way for large-scale phenotyping of root metabolism and signaling.
Chicken serum albumin (Gal d 5 * ) is a partially heat‐labile inhalant and food allergen implicated in the bird‐egg syndrome

Background: Chicken serum albumin (α‐livetin) has been implicated as the causative allergen of the bird‐egg syndrome. However, the clinical relevance of sensitization to this allergen has not been confirmed by specific challenge tests and environmental sampling. We investigated whether chicken albumin can be detected in air samples collected in a home with birds, and whether sensitization to this protein may cause respiratory and food allergy symptoms. The heat resistance of chicken albumin and the possible cross‐reactivity with conalbumin were also investigated.
Proteins of calcified endoskeleton: II Partial amino acid sequences of endoskeletal proteins and the characterization of proteinaceous organic matrix of spicules from the alcyonarian, Synularia polydactyla

Calcified organic substances in the skeleton contain a protein‐polysaccharide complex taking a key role in the regulation of bio‐calcification. However, information concerning the matrix proteins in alcyonarian and their effect on calcification process is still unknown. For this reason, we have studied the organic matrix of endoskeletal spicules from the alcyonarian coral, Synularia polydactyla, to analyze the proteins with their sequences and investigate the functional properties by a molecular approach. The separated spicules from the colony were identified by scanning electron microscope (SEM). The soluble organic matrix comprised 0.04% of spicule weight. By recording decline of pH in the experimental design, the inhibitory effect of the matrix on CaCO3 precipitation was revealed. Prior to electrophoresis, our analysis of proteins extracted from the soluble organic matrix of the spicules revealed an abundance of proteins in molecular weight. The sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) analysis of the preparations showed seven bands of proteins with an apparent molecular mass of 109, 83, 70, 63, 41, 30 and 22 kDa. The proteins were electrophoresed on Tricine‐SDS‐PAGE after electro‐elution treatment, and then transferred to polyvinylidene difluoride (PVDF) membranes and their N‐termini were sequenced. Two bands of proteins of about 70 and 63 kDa successfully underwent N‐terminal amino acid sequencing. For the detection of calcium binding proteins, a Ca2+ overlay analysis was conducted on the extract by 45Ca autoradiography. The 109 and 63 kDa calcium binding proteins were found to be radioactive. Periodic acid schiff staining indicated that 83 and 63 kDa proteins were glycosylated. An assay for carbonic anhydrase, which is thought to play an important role in the process of calcification revealed low level of the activity. These findings suggest that the endoskeletal spicules of alcyonarian corals have protein‐rich organic matrices, which might be related to the calcification process.
Treatment of a Patient With Task-Specific Writing Tremor Using Magnetic Resonance-Guided Focused Ultrasound

Abstract Task-specific dystonia is characterized by abnormal repetitive movements or postures in a specific body part that is triggered and ends with a task, such as writing. Failing medications, surgery, specifically disruption of key nuclei in the thalamus, can provide excellent symptomatic relief. Transcranial magnetic resonance (MR)-guided focused ultrasound is an emerging incision-less thermoablation technique. We describe MR-guided focused ultrasound tandem ablation of the ventral intermediate and ventralis oralis posterior nuclei in a 60-year-old patient with writer’s cramp. The clinical improvement was immediate with incremental benefit from the latter lesion, which was sustained at 6 months follow-up. RÉSUMÉ Traitement d’un patient atteint de tremblement de l’écriture lié à une tâche spécifique en utilisant des ultrasons concentrés guidés par résonnance magnétique. La dystonie relative à une tâche particulière se caractérise par des postures ou des mouvements anormaux et répétitifs qui affectent une partie spécifique du corps. Ces mouvements sont provoqués lors de l’exécution d’une tâche, par exemple l’écriture, et cessent quand cette tâche se conclut. Pour contrer ce trouble moteur, des traitements médicamenteux ainsi que la chirurgie, c’est-à-dire l’ablation d’une partie du noyau central du thalamus, peuvent procurer un très bon soulagement symptomatique. Cela étant, l’utilisation transcrânienne d’ultrasons concentrés guidés par résonnance magnétique constitue une nouvelle technique de thermoablation qui exclut toute forme d’incision. Notre intention est ici de décrire l’ablation consécutive, au moyen d’ultrasons concentrés guidés par résonnance magnétique, des noyaux ventral médian et oral postérieur dans le cas d’un patient âgé de 60 ans aux prises avec des crampes liées à l’écriture. Si l’amélioration clinique s’est révélée rapide, les bénéfices encourus se sont également révélés durables lors d’un suivi six mois après l’intervention.
Direct assay for cobalamin bound to transcobalamin (holo-transcobalamin) in serum.

BACKGROUND Only cobalamin carried by transcobalamin (holo-transcobalamin) is available for cellular uptake and hence is physiologically relevant. However, no reliable or accurate methods for quantifying holo-transcobalamin are available. We report a novel holo-transcobalamin assay based on solid-phase capture of transcobalamin. METHODS A monoclonal antibody specific for human transcobalamin with an affinity constant >10(10) L/mol was immobilized on magnetic microspheres to capture and concentrate transcobalamin. The cobalamin bound to transcobalamin was then released and assayed by a competitive binding radioassay. The quantification of holo-transcobalamin was accomplished using calibrators composed of recombinant, human holo-transcobalamin. RESULTS The assay was specific for holo-transcobalamin and had a detection limit of 5 pmol/L. Within-run and total imprecision (CV) was 5% and 8-9%, respectively. The working range (CV <20%) was 5-370 pmol/L. Dilutions of serum were linear in the assay range. The recovery of recombinant, human holo-transcobalamin added to serum was 93-108%. A 95% reference interval of 24-157 pmol/L was established for holo-transcobalamin in 105 healthy volunteers 20-80 years of age. For 72 of these sera, holo-haptocorrin and total cobalamin were also determined. Whereas holo-haptocorrin correlated well (r(2) = 0.87) with total cobalamin, holo-transcobalamin correlated poorly (r(2) = 0.23) with total cobalamin or holo-haptocorrin. CONCLUSIONS The solid-phase capture assay provides a simple, reliable method for quantitative determination of holo-transcobalamin in serum.
Improving audio-visual speech recognition using deep neural networks with dynamic stream reliability estimates

Audio-visual speech recognition is a promising approach to tackling the problem of reduced recognition rates under adverse acoustic conditions. However, finding an optimal mechanism for combining multi-modal information remains a challenging task. Various methods are applicable for integrating acoustic and visual information in Gaussian-mixture-model-based speech recognition, e.g., via dynamic stream weighting. The recent advances of deep neural network (DNN)-based speech recognition promise improved performance when using audio-visual information. However, the question of how to optimally integrate acoustic and visual information remains. In this paper, we propose a state-based integration scheme that uses dynamic stream weights in DNN-based audio-visual speech recognition. The dynamic weights are obtained from a time-variant reliability estimate that is derived from the audio signal. We show that this state-based integration is superior to early integration of multi-modal features, even if early integration also includes the proposed reliability estimate. Furthermore, the proposed adaptive mechanism is able to outperform a fixed weighting approach that exploits oracle knowledge of the true signal-to-noise ratio.
Estimation of genetic risk for type 1 diabetes.

The most important gene loci defining risk of type 1 diabetes mellitus (T1DM) are located within the HLA gene region. HLA-DQ molecules are of primary importance but HLA-DR gene products modify the risk conferred by HLA-DQ. The risk associated with an HLA genotype is defined by the particular combination of susceptible and protective alleles. The highest risk is associated with a combination of two different risk haplotypes (7% risk to develop T1DM in Finland) whereas protective genotypes covering 69% of population have a risk of less than 0.2%). The complicated analysis of HLA genotypes is simplified by strong linkage disequilibrium between HLA-DRB1, -DQA1 and -DQB1 loci. In many cases one can deduce the alleles of other loci based on determination of the alleles in one locus. Differences between various populations in the frequency of marker alleles and in the linkages between them has to be taken into account. We have developed PCR based typing methods that utilize blood spot samples, microtiter plate format and lanthanide labeled oligonucleotide probes to define HLA-DQ and -DR alleles relevant for T1DM risk. Typing is run stepwise so that after initial HLA-DQB1 typing only those samples will be further analyzed in which -DQA1 or -DRB1 typing is informative and expected to contribute to the risk estimation. This method has been used to screen more than 50,000 newborn infants in Finland over a time period of 6 years, and it has been able to identify most children who have developed T1D during the follow-up period. The efficiency of the procedure has also been tested in Finnish and Greek populations.
Characterization of Metabolites in the Biotransformation of 2,4,6-Trinitrotoluene with Anaerobic Sludge: Role of Triaminotoluene

ABSTRACT The present study describes the biotransformation of 2,4,6-trinitrotoluene (TNT) (220 μM) by using anaerobic sludge (10%, vol/vol) supplemented with molasses (3.3 g/liter). Despite the disappearance of TNT in less than 15 h, roughly 0.1% of TNT was attributed to mineralization (14CO2). A combination of solid-phase microextraction–gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry identified two distinctive cycles in the degradation of TNT. One cycle was responsible for the stepwise reduction of TNT to eventually produce triaminotoluene (TAT) in relatively high yield (160 μM). The other cycle involved TAT and was responsible for the production of azo derivatives, e.g., 2,2′,4,4′-tetraamino-6,6′-azotoluene (2,2′,4,4′-TA-6,6′-azoT) and 2,2′,6,6′-tetraamino-4,4′-azotoluene (2,2′,6,6′-TA-4,4′-azoT) at pH 7.2. These azo compounds were also detected when TAT was treated with the anaerobic sludge but not with an autoclaved sludge, suggesting the biotic nature of their formation. When the anaerobic conditions in the TAT-containing culture medium were removed by aeration and/or acidification (pH 3), the corresponding phenolic compounds, e.g., hydroxy-diaminotoluenes and dihydroxy-aminotoluenes, were observed at room temperature. Trihydroxytoluene was detected only after heating TAT in water at 100°C. When 13CH3-labeled TNT was used as the N source in the above microcosms, we were unable to detect13C-labeled p-cresol or [13CH3]toluene, indicating the absence of denitration or deamination in the biodegradation process. The formation and disappearance of TAT were not accompanied by mineralization, suggesting that TAT acted as a dead-end metabolite.
The spectral gap of dense random regular graphs

For any $\alpha\in (0,1)$ and any $n^{\alpha}\leq d\leq n/2$, we show that $\lambda(G)\leq C_\alpha \sqrt{d}$ with probability at least $1-\frac{1}{n}$, where $G$ is the uniform random $d$-regular graph on $n$ vertices, $\lambda(G)$ denotes its second largest eigenvalue (in absolute value) and $C_\alpha$ is a constant depending only on $\alpha$. Combined with earlier results in this direction covering the case of sparse random graphs, this completely settles the problem of estimating the magnitude of $\lambda(G)$, up to a multiplicative constant, for all values of $n$ and $d$, confirming a conjecture of Vu. The result is obtained as a consequence of an estimate for the second largest singular value of adjacency matrices of random {\it directed} graphs with predefined degree sequences. As the main technical tool, we prove a concentration inequality for arbitrary linear forms on the space of matrices, where the probability measure is induced by the adjacency matrix of a random directed graph with prescribed degree sequences. The proof is a non-trivial application of the Freedman inequality for martingales, combined with boots-trapping and tensorization arguments. Our method bears considerable differences compared to the approach used by Broder, Frieze, Suen and Upfal (1999) who established the upper bound for $\lambda(G)$ for $d=o(\sqrt{n})$, and to the argument of Cook, Goldstein and Johnson (2015) who derived a concentration inequality for linear forms and estimated $\lambda(G)$ in the range $d= O(n^{2/3})$ using size-biased couplings.
Intracellular Bacterial Infections: A Challenge for Developing Cellular Mediated Immunity Vaccines for Farmed Fish

Aquaculture is one of the most rapidly expanding farming systems in the world. Its rapid expansion has brought with it several pathogens infecting different fish species. As a result, there has been a corresponding expansion in vaccine development to cope with the increasing number of infectious diseases in aquaculture. The success of vaccine development for bacterial diseases in aquaculture is largely attributed to empirical vaccine designs based on inactivation of whole cell (WCI) bacteria vaccines. However, an upcoming challenge in vaccine design is the increase of intracellular bacterial pathogens that are not responsive to WCI vaccines. Intracellular bacterial vaccines evoke cellular mediated immune (CMI) responses that “kill” and eliminate infected cells, unlike WCI vaccines that induce humoral immune responses whose protective mechanism is neutralization of extracellular replicating pathogens by antibodies. In this synopsis, I provide an overview of the intracellular bacterial pathogens infecting different fish species in aquaculture, outlining their mechanisms of invasion, replication, and survival intracellularly based on existing data. I also bring into perspective the current state of CMI understanding in fish together with its potential application in vaccine development. Further, I highlight the immunological pitfalls that have derailed our ability to produce protective vaccines against intracellular pathogens for finfish. Overall, the synopsis put forth herein advocates for a shift in vaccine design to include CMI-based vaccines against intracellular pathogens currently adversely affecting the aquaculture industry.
Effect of exercise on insulin action, glucose tolerance, and insulin secretion in aging.

To assess the effect of exercise training on the insulin resistance and impaired pancreatic B-cell function of aging, we studied 13 healthy older men (ages 61-82 yr) before and after 6 mo intensive endurance exercise. An index of insulin sensitivity (SI) was measured using Bergman's minimal model. Intravenous glucose tolerance was quantified using the glucose disappearance constant (KGlc) while oral glucose tolerance was assessed after a 100-g glucose load. B-cell function was evaluated by measuring the acute insulin response (AIR) to glucose injection at fasting glucose (AIRGlc) and the AIR to arginine at multiple clamped glucose levels. Exercise produced an endurance training effect as demonstrated by an 18% increase in maximum O2 consumption (VO2max) [38.2 +/- 1.4 to 45.0 +/- 1.1 (SE) ml.kg fat-free mass-1.min-1, P less than 0.001]. An unchanged fasting glucose (5.3 +/- 0.2 to 5.4 +/- 0.2 mM) despite a reduced fasting insulin (61 +/- 6 to 48 +/- 6 pM, P less than 0.01) suggested exercise training improved insulin sensitivity. This was confirmed by a 36% increase in SI from 3.47 +/- 0.41 to 4.71 +/- 0.42 x 10(-5) min-1/pM (P = 0.01). Intravenous glucose tolerance did not change as measured by KGlc, which was 1.46 +/- 0.09 before and 1.48 +/- 0.16%/min after exercise training. Likewise, the incremental glucose response to oral glucose (633 +/- 49-618 +/- 45 mM.min) was unchanged. B-cell function was decreased as reflected by AIRGlc (351 +/- 73-245 +/- 53 pM, P less than 0.01) and the AIRArg at maximal glycemic potentiation (AIRmax, 1,718 +/- 260-1,228 +/- 191 pM, P less than 0.005). (ABSTRACT TRUNCATED AT 250 WORDS)
High-Intensity Running and Energy Restriction Reduce Postprandial Lipemia in Girls.

PURPOSE This study examined the potency of combining acute high-intensity exercise and energy intake restriction on postprandial triacylglycerol concentrations ([TAG]) in healthy girls. METHODS Sixteen 11- to 13-yr-old girls (mean (SD) body mass, 45.1 (7.6) kg; peak oxygen uptake (V˙O2), 43 (6) mL·kg(-1)·min(-1)) completed three 2-d conditions in a counterbalanced crossover design separated by 14 d. On day 1, participants completed 10 × 1-min interval runs (HIIR) or 5 × 1-min interval runs combined with 0.82 (0.19) MJ energy intake restriction (HIIR-ER) or rested (CON). Exercise was completed at 100% maximal aerobic speed determined from an incremental peak V˙O2 test, with 1-min recovery between intervals. On day 2, capillary blood samples were taken in the fasted state and at predetermined intervals throughout the 6.5-h postprandial period. A standardized breakfast and lunch were consumed immediately and 4 h after the fasting sample, respectively. RESULTS Based on ratios of the geometric means (95% confidence intervals (CI) for ratios), fasting [TAG] was 16% and 8% lower than CON in HIIR (-24% to -7%; effect size (ES), 0.49; P = 0.002) and HIIR-ER (-17% to 1%; ES, 0.24; P = 0.09), respectively; HIIR was 8% lower than HIIR-ER (-17% to 1%; ES, 0.25; P = 0.08). The total area under the [TAG] versus time curve was 10% and 9% lower than CON in HIIR (-16% to -3%; ES, 0.30; P = 0.01) and HIIR-ER (-15% to -2%; ES, 0.28; P = 0.01), respectively; HIIR-ER and HIIR were similar (-1%; -8% to 6%; P = 0.80). CONCLUSIONS Manipulations of HIIR and ER reduce postprandial [TAG] in girls. The magnitude of effect was marginally, although not meaningfully, greater after HIIR than that after HIIR-ER.