Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of Tyrosine 320 Impairs Spontaneous Endocytosis and Enhances Release of HLA-B27 Molecules

Several lines of evidence suggest that endocytosis of MHC class I molecules requires conserved motifs within the cytoplasmic domain. In this study, we show, in the C58 rat thymoma cell line transfected with HLA-B27 molecules, that replacement of the highly conserved tyrosine (Tyr320) in the cytoplasmic domain of HLA-B27 does not hamper cell surface expression of β2-microglobulin H chain heterodimers or formation of misfolded molecules. However, Tyr320 replacement markedly impairs spontaneous endocytosis of HLA-B27. Although wild-type molecules are mostly internalized via endosomal compartments, Tyr320-mutated molecules remain at the plasma membrane in which partial colocalization with endogenous transferrin receptors can be observed, also impairing their endocytosis. Finally, we show that Tyr320 substitution enhances release of cleaved forms of HLA-B27 from the cell surface. These studies show for the first time that Tyr320 is most likely part of a cytoplasmic sorting motif involved in spontaneous endocytosis and shedding of MHC class I molecules.
Changes in macrophyte communities in Lake Swarzędzkie after the first year of restoration

Abstract Lake Swarzędzkie, near Poznań, was a hypertrophic lake because of its high nutrient content, cyanobacteria blooms, and disruptive recreational use, especially swimming, which was popular there. This is why protection measures have been in place since 1991, and a restoration program has been ongoing since fall 2011. The evaluation of the presence and distribution of macrophytes as an important element of lake ecosystem was conducted in August 2012. Nine plant communities were observed: Phragmitetum communis; Typhetum angustifoliae; Nupharo-Nymphaeetum albae; Hydrocharitetum morsus-ranae; Thelypteridi-Phragmitetum; Cicuto-Caricetum pseudocyperi; Acoretum calami; Ceratophylletum demersi; Potametum lucentis. The first three were dominating associations. The presence of submerged vegetation appears to verify the positive impact of the applied conservation and restoration measures. Improvement is confirmed by the significant decrease in concentrations of chlorophyll-a and total nitrogen, as well as the gradual decrease in total suspended solids and increased transparency.
Biochemical studies of bacterial sporulation and germination. V. Purine nucleoside phosphorylase of vegetative cells and spores of Bacillus cereus.

Abstract 1. Purine nucleoside phosphorylase was purified from the vegetative cells and spores of Bacillus cereus var. terminalis. The enzymes from the vegetative cell and the spore were found to have similar physical and catalytic properties. A mutant (strain 29) with only 2% of the level of enzyme activity in the vegetative cell also had a comparably low level in the spore. 2. The vegetative cell enzyme is inducible by inosine. Nevertheless, sporulation in the absence of inducer leads to high enzyme levels in the sporulating cell and spore, presumably due to endogenous changes during the stationary phase preceding spore development. The enzyme activity in mutant strain 29 appeared to be constitutive. 3. Spores of mutant strain 29 with only 3% of the level of enzyme activity of wild type spores germinated in response to inosine as rapidly and as completely as did the wild type spores.
Circulating miR-195 as a Therapeutic Biomarker in Turkish Breast Cancer Patients.

BACKGROUND Dysregulation of miRNA expression may be used as a biomarker for specific tumours because it may contribute to development of cancer. Circulating miRNA profiles have been highlighted for their potential as predictive markers in heterogeneous diseases such as breast cancer. In the literature, there is evidence that miR-195 levels are differentially expressed pre- and post-operative periods in breast cancer patients. At the same time, miRNA expression levels may vary because of ethnic origins. This study aimed to determine expression levels and potential roles of miR-195 in Turkish breast cancer patients. MATERIALS AND METHODS The expression patterns of miR-195 were initially examined in breast cancer tissues (luminal A and B type) (n=96). Subsequently, blood samples were prospectively collected from preoperative and postoperative Turkish breast cancer patients and disease free controls. Total RNA was isolated, and the expression level of miR-195 was quantified by real-time PCR. RESULTS We found that miR-195 level was altered in Turkish breast cancer patients, with down-regulation evident in breast cancer tissues compared to normal adjacent specimens. Furthermore, circulating levels of miR- 195 was significantly decreased in post-operative blood samples compared with pre-operative levels (p=0.01 and <0.05). However, miR-195 was significantly increased in pre-operative blood samples of the luminal B type (p= 0.04 and <0.05). CONCLUSIONS This study represents the first report of a miR-195 expression profile in Turkish breast cancer patients. Our data suggests that miR-195 levels might be a clinically useful biomarker in the earliest stage of Turkish breast cancer patients.
Preparation of procoligenoids from Escherichia coli heat-labile enterotoxins

Heat-labile enterotoxins from Escherichia coli strains of porcine and human origin polymerize on heating to form high-molecular-weight aggregates, "procoligenoids," analogous to procholeragenoid derived from the cholera enterotoxin. This aggregation is accompanied by loss of biological activity (toxicity). Further heating results in the release of B-subunit oligomers, coligenoids, analogous to choleragenoid. Further studies are needed to determine whether, like procholeragenoid, the procoligenoids are superior antigens in stimulating gut immunity after parenteral administration.
Longitudinal Mechano-Sorptive Creep Behavior of Chinese Fir in Tension during Moisture Adsorption Processes

To provide comprehensive data on creep behaviors at relative humidity (RH) isohume conditions and find the basic characteristics of mechano-sorptive (MS) creep (MSC), the tensile creep behaviors, “viscoelastic creep (VEC)” at equilibrium moisture content and MSC during adsorption process, were performed on Chinese fir in the longitudinal direction under 20%, 40%, 60% and 80% RH (25 °C) and at 1, 1.3, and 1.6 MPa, respectively. The free swelling behavior was also measured, where the climate conditions corresponded with MSC tests. Based on the databases of free swelling, VEC, and MSC, the existence of MS effect was examined, and the application of the rheological model under the assumption of partitioned strain was investigated. The results revealed that both VEC and MSC increased with magnitude of applied stress, and the increasing RH level. Under all RH isohume conditions, the total strain of MSC was greater than that of VEC. The influence of RH level on VEC was attributed to the water plasticization effect, whereas that on MSC was presumed to be the effect of water plasticization and unstable state in the wood cell wall. In addition, the RH level promoted the relaxation behavior in MSC, while it slightly affected the relaxation behavior in VEC. In the future, the rheological model could consider the link between load configuration and the anatomic structural feature of wood.
A Novel Ultrasonic Resonance Field Device for the Retention of Animal Cells

This article describes two types of flow‐through cell retention devices based on the concept of layered piezoelectric resonators. A single‐chamber device is compared to a novel optimized steam‐sterilizable prototype ultrasonic cell separator with improved acoustic design and an integrated cooling circuit, eliminating the problem of local temperature increase caused by the high amplitudes necessary to achieve the separation of animal cells with low acoustic contrast. This setup yields highly reproducible results and is ideal for studying the long‐term effects of ultrasonic sound fields and separation efficiency. The novel two‐chamber system has the potential for scaleability due to the reduction in thermal and acoustic flow, increased field stability, and separation efficiency. Finally, the effect of power input on separation and cell viability is reported. Such flow‐through cell retention systems could be used as systems to retain biomass within the fermentor or as a substitute for centrifugation, with the major advantage of eliminating high‐speed rotational motion.
Long-Term Stability of Aluminum Oxide Based Surface Passivation Schemes Under Illumination at Elevated Temperatures

The stability of passivation layers under the conditions of field application of solar modules is a crucial parameter. We have performed an experiment to test the stability of aluminum oxide based passivation schemes under halogen lamp illumination of 1 sun equivalent intensity at 75 °C. We compare aluminum oxide layers with atomic layer deposition and plasma-enhanced chemical vapor deposition with and without an amorphous silicon nitride capping layer. Different thermal treatments are performed to activate the passivation or simulate solar cell contact firing. All passivation schemes are tested on full four inch 1 Ω·cm p- and n-type float-zone silicon wafers. The quality and stability of the surface passivation are tested by means of repeated charge carrier lifetime measurements. No significant surface passivation degradation due to light-soaking is evident on capped samples for several hundred hours. N-type samples are demonstrated to maintain excellent passivation quality for at least 3700 h and only slight degradation of p-type samples is found.
Lytic metastases in thoracolumbar spine: computer-aided detection at CT--preliminary study.

PURPOSE To evaluate the sensitivity of a computer-aided detection (CAD) system for detection of lytic thoracolumbar spinal lesions at body CT, with results of manual lesion segmentation as the reference standard. MATERIALS AND METHODS The study was HIPAA compliant and institutional review board approved; the institutional review board waived the need for informed consent. The CAD system segments the spine on CT images and searches for detections that match size, shape, location, and attenuation criteria. To reduce false-positive findings, 16 features for each detection were computed and fed to a classifier trained with manually segmented lesions. The data set consisted of CT studies of 50 patients (30 men, 20 women; range, 18-82 years; mean, 54.8 years) with 28 lesions. Studies were assigned to either a training (29 studies) or testing (21 studies) set. Sensitivities and false-positive rates (FPRs) for training and testing sets were calculated for these lesions, which were probable lytic metastases with areas 0.8 cm(2) or greater. RESULTS Training set sensitivity was 0.83 (10 of 12; 95% confidence interval: 0.51, 0.97), with an FPR of 7.4 per patient. Test set sensitivity was 0.94 (15 of 16; 95% confidence interval: 0.68, 1.00), with an FPR of 4.5 per patient. There was no significant difference between the CAD sensitivities of the training and test sets (P = .56). Of three false-negative findings, two were due to incomplete segmentation of the vertebral pedicle, and the third was rejected by the classifier. False-positive detections were most often attributable to veins that connect the basivertebral vein with the anterior venous plexus (106 [34%] of 310) and to low-attenuating disks (83 [27%] of 310). CONCLUSION This CAD system successfully identified probable lytic metastases in the thoracolumbar spine and generalized well to an independent testing set.
Absolute and Relative Contraindications to IV rt-PA for Acute Ischemic Stroke

Most of the contraindications to the administration of intravenous (IV) recombinant tissue plasminogen activator (rtPA) originated as exclusion criteria in major stroke trials. These were derived from expert consensus for the National Institute of Neurological Disorders and Stroke (NINDS) trial. Despite the fact that the safety and efficacy of IV rtPA has been repeatedly confirmed in large international observational studies over the past 20 years, most patients with acute ischemic stroke disappointingly still do not receive thrombolytic treatment. Some of the original exclusion criteria have proven to be unnecessarily restrictive in real-world clinical practice. It has been suggested that application of relaxed exclusion criteria might increase the IV thrombolysis rate up to 20% with comparable outcomes to thrombolysis with more conventional criteria. We review the absolute and relative contraindications to IV rtPA for acute ischemic stroke, discussing the underlying rationale and evidence supporting these exclusion criteria.
Initial Progress in Transfer for Deep Reinforcement Learning Algorithms

As one of the first successful models that combines reinforcement learning technique with deep neural networks, the Deep Q-network (DQN) algorithm has gained attention as it bridges the gap between high-dimensional sensor inputs and autonomous agent learning. However, one main drawback of DQN is the long training time required to train a single task. This work aims to leverage transfer learning (TL) techniques to speed up learning in DQN. We applied this technique in two domains, Atari games and cart-pole, and show that TL can improve DQN’s performance on both tasks without altering the network structure.
Influence of population density and climate on the demography of subalpine golden-mantled ground squirrels

Abstract Temporal fluctuation in abundance is common in many wildlife populations, but the causes and consequences to population dynamics of these fluctuations remain poorly understood. We used long-term (1990–2008) field data to investigate the influence of population size and environmental factors (climatic variables and predation) on the demography of golden-mantled ground squirrels (Callospermophilus lateralis). Survival varied by sex and age class, with highest survival for adult females (Φ = 0.519, 95% confidence interval [95% CI] = 0.462–0.576) and lowest survival for juvenile males (Φ = 0.120, 95% CI = 0.094–0.152). Population size negatively influenced survival with a time lag of 1 year. Among environmental factors, current year's rainfall and intensity of predation substantially influenced survival. Probability of successful reproduction (probability that a female weans ≥1 pups) was higher for older females (Ψ = 0.816, 95% CI = 0.734–0.877) than for yearlings (Ψ = 0.313, 95% CI = 0.228–0.412). Rainfall negatively influenced probability of successful reproduction of both older and yearling females with a time lag of 1 year. Litter size ranged from 1 to 8 pups, with a mean of 4.8 (95% CI = 4.5–5.1). We found no evidence that litter size varied among age classes or over time, or was influenced by population size or environmental factors. Our results suggest that population size and environmental factors do not affect all demographic variables in the same way, and that both density-dependent and environmental factors influence the size of our study population.
Histone deacetylase 1, 2, 6 and acetylated histone H4 in B‐ and T‐cell lymphomas

Aims: Histone deacetylase (HDAC) inhibitors are novel therapeutics in the treatment of peripheral T‐cell lymphoma, unspecified (PTCL) and diffuse large B‐cell lymphoma (DLBCL), where, for unknown reasons, T‐cell malignancies appear to be more sensitive than B‐cell malignancies. The aim was to determine HDAC expression in DLBCL and PTCL which has not previously been investigated.
The Contribution of the Medial Prefrontal Cortex, Orbitofrontal Cortex, and Dorsomedial Striatum to Behavioral Flexibility

Abstract: Behavioral flexibility refers to the ability to shift strategies or response patterns with a change in environmental contingencies. The frontal lobe and basal ganglia are two brain regions implicated in various components for successfully adapting to changed environmental contingencies. This paper discusses a series of experiments that investigate the contributions of the rat prelimbic area, infralimbic area, orbitofrontal cortex, and dorsomedial striatum to behavioral flexibility. Orbitofrontal cortex inactivation did not impair initial learning of discrimination tests, but it impaired reversal learning due to perseverance in the previously learned choice pattern. Inactivation of the prelimbic area did not affect acquisition or reversal learning of different discrimination tests, but it selectively impaired learning when rats had to inhibit one strategy and shift to using a new strategy. However, comparable to orbitofrontal cortex inactivation, strategy‐switching deficits following prelimbic inactivation resulted from a perseverance of the previously relevant strategy. Fewer studies have examined the infralimbic region, but there is some evidence suggesting that this region supports reversal learning by maintaining the reliable execution of a new choice pattern. Dorsomedial striatal inactivation impaired both reversal learning and strategy switching. The behavioral flexibility deficits following dorsomedial striatal inactivation resulted from the inability to maintain a new choice pattern once selected. Taken together, the results suggest that orbitofrontal and prelimbic subregions differentially contribute to behavioral flexibility, but they are both critical for the initial inhibition of a previously learned strategy, while the dorsomedial striatum plays a broader role in behavioral flexibility and supports a process that allows the reliable execution of a new strategy once selected.
Ultrastructural analysis of root canal dentine irradiated with 980-nm diode laser energy at different parameters.

OBJECTIVE The purpose of this in vitro study was to investigate using the scanning electron microscope (SEM) the ultrastructural morphological changes of the radicular dentine surface after irradiation with 980-nm diode laser energy at different parameters and angles of incidence. BACKGROUND DATA There have been limited reports on the effects of diode laser irradiation at 980 nm on radicular dentin morphology. MATERIALS AND METHODS Seventy-two maxillary canines were sectioned and roots were biomechanically prepared using K3 rotary instruments. The teeth were irrigated with 2 mL of distilled water between files and final irrigation was performed with 10 mL of distilled water. The teeth were then randomly divided into five groups (n = 8 each) according to their diode laser parameters: Group 1: no irradiation (control); group 2: 1.5 W/continuous wave (CW) emission (the manufacturer's parameters); group 3: 1.5 W/100 Hz; group 4: 3 W/CW; and group 5: 3 W/100 Hz. Laser energy was applied with helicoid movements (parallel to the canal walls) for 20 sec. Eight additional teeth for each group were endodontically prepared and split longitudinally and irradiation was applied perpendicularly to the root surface. RESULTS Statistical analysis showed no difference between the root canal thirds irradiated with the 980-nm diode laser, and similar results between the parameters 1.5 W/CW and 3 W/100 Hz (p > 0.05). CONCLUSION When considering different output powers and delivery modes our results showed that changes varied from smear layer removal to dentine fusion.
CLINICAL INFERENCES AND DECISIONS—I. DIAGNOSIS AND BAYES‘ THEOREM

Abstract Clinical decisions are based upon inferences derived from test evidence where data is collected as a means of hypothesis testing. In medicine, the initial expectation of a clinical state is rarely expressed in the classical scientific language of a null hypothesis where alternative outcomes are assumed to be equally probable, because clinical experience reinforces the maxim that common events occur commonly. The collection of test evidence in clinical practice, therefore, is directed towards overturning prior likelihoods for a clinically pathological state which are far from mere chance expectations. The extent to which any test evidence can modify such prior expectations not only depends on its relevance to the clinical state in question (i.e. the hypothesis) but also is largely influenced by the inherent error rates in the test itself. Clinical decision models should reflect these facts. Using examples from the field of ophthalmology, this paper presents a normative model using Bayes' theorem of conditional probabilities which provides a rational framework upon which to base or appraise clinical decisions. Parts II and III of the series will expand this clinical application of decision theory to show how it may be used in the absence of hard test evidence and also where a different emphasis or utility may be placed on false positive or false negative errors.
Remaining useful life prediction of rolling element bearings based on health state assessment

Instead of looking for an overall regression model for remaining useful life (RUL) prediction, this paper proposes a RUL prediction framework based on multiple health state assessment that divides the entire bearing life into several health states where a local regression model can be built individually. A hybrid approach consisting of both unsupervised learning and supervised learning is proposed to automatically estimate the real-time health state of a bearing in cases with no prior knowledge available. Support vector machine is the main technology adopted to implement health state assessment and RUL prediction. Experimental results on accelerated degradation tests of rolling element bearings demonstrate the effectiveness of the proposed framework.
Behavior of non-protein-bound and protein-bound uremic solutes during daily hemodialysis.

BACKGROUND In the last few years, renewed interest in daily short hemodialysis (DHD; six 2-hour sessions per week) has become apparent as a consequence of the better clinical outcome of patients treated by this schedule. Uremic syndrome is characterized by the retention of a large number of toxins with different molecular masses and chemical properties. Some toxins are water soluble and non-protein bound, whereas others are partially lipophilic and protein bound. There is increased evidence that protein-bound toxins are responsible for the biochemical and functional alterations present in uremic syndrome, and the kinetics of urea is not applicable to these substances for their removal. The aim of this study is to investigate whether DHD is accompanied by increased removal of non-protein-bound and protein-bound toxins and a decrease in their prehemodialysis (pre-HD) serum levels. PATIENTS AND METHODS We studied 14 patients with end-stage renal disease treated by standard HD (SHD; three 4-hour sessions per week) for at least 6 months and randomly assigned them to a two-period crossover study (SHD to DHD and DHD to SHD). Patients maintained the same dialyzer, dialysate, and Kt/V during the entire study. At the end of 6 months of SHD and 6 months of DHD, we evaluated hemoglobin levels, hematocrits, recombinant human erythropoietin doses, and pre-HD and post-HD concentrations of serum urea, creatinine, uric acid, and the following protein-bound toxins: 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, p-cresol, indole-3-acetic acid, indoxyl sulfate, and hippuric acid. RESULTS Values for hemoglobin, hematocrit, and recombinant human erythropoietin dose did not change during the two study periods. Pre-HD concentrations of creatinine, urea, and uric acid decreased on DHD (creatinine, from 8.7 +/- 1.9 to 7.8 +/- 1.6 mg/dL; P < 0.05; urea, from 149.4 +/- 28.8 to 132.7 +/- 40 mg/dL; P = 0.05; uric acid, from 9.14 +/- 1.49 to 8.16 +/- 1.98 mg/dL; P = 0.06). Concerning protein-bound toxins, lower pre-HD levels during DHD were reported for indole-3-acetic acid (SHD, 0.16 +/- 0.04 mg/dL; DHD, 0.13 +/- 0.03 mg/dL; P = 0.01), indoxyl sulfate (SHD, 3.35 +/- 1.68 mg/dL; DHD, 2.85 +/- 1.08 mg/dL; P = 0.02), and p-cresol at the borderline of significance (SHD, 0.96 +/- 0.59 mg/dL; DHD, 0.78 +/- 0.33 mg/dL; P = 0.07). CONCLUSION Such non-protein-bound compounds as uric acid, creatinine, and urea were removed significantly better by DHD, and pre-HD serum levels were reduced. Furthermore, pre-HD concentrations of some protein-bound solutes, such as indole-3-acetic acid, indoxyl sulfate, and p-cresol, also were lower during DHD.