Miracle-dz/UniFAR-FTUs huggingface dataset:
2016 Comprehensive Update of the Banff Working Group on Liver Allograft Pathology: Introduction of Antibody‐Mediated Rejection

The Banff Working Group on Liver Allograft Pathology reviewed and discussed literature evidence regarding antibody‐mediated liver allograft rejection at the 11th (Paris, France, June 5–10, 2011), 12th (Comandatuba, Brazil, August 19–23, 2013), and 13th (Vancouver, British Columbia, Canada, October 5–10, 2015) meetings of the Banff Conference on Allograft Pathology. Discussion continued online. The primary goal was to introduce guidelines and consensus criteria for the diagnosis of liver allograft antibody‐mediated rejection and provide a comprehensive update of all Banff Schema recommendations. Included are new recommendations for complement component 4d tissue staining and interpretation, staging liver allograft fibrosis, and findings related to immunosuppression minimization. In an effort to create a single reference document, previous unchanged criteria are also included.
Post-injury and resolution response to repetitive inhalation exposure to agricultural organic dust in mice

Inhalation of organic dusts in agricultural environments causes airway inflammatory diseases. Despite advances in understanding the airway response to dust-induced inflammation, less is known about the transition from lung injury to repair and recovery. The objective of this study was to define the post-inflammation homeostasis events following organic dust-induced lung injury. Using an established protocol, mice were intranasally treated with swine confinement facility organic dust extract (ODE) daily for 3 weeks (repetitive exposure) or treated daily with ODE for 3 weeks followed by no treatment for 1–4 weeks (recovery period) whereupon lavage fluid, lung tissue, and sera were processed. During recovery period, a significant decrease was observed in ODE-induced neutrophil levels after 1 week, lymphocytes at 2 weeks, and macrophages at 4 weeks in the lavage fluid. ODE-induced lung cellular aggregates and bronchiolar compartment inflammation were diminished, but persisted for 4 weeks post-injury. Alveolar inflammation resolved at 3 weeks. ODE-induced lung neutrophils were cleared by 3 weeks, B-cells by 2 weeks, and CD3+CD4+ and CD3+CD8+ T cells by 4 week recovery period. Collectively, these results identify important processes during recovery period following agricultural dust-induced inflammation, and present possible strategies for improving lung repair and resolution.
Variation of the Magnetic Properties of Sm (Co, Cu)5 Alloys with Temperature

Modified permanent magnets of rare earth cobalt compounds, R(Co, Cu)5, are known as alloys having a complex decomposition mechanism. Studies of the variation of magnetic properties with temperature were carried out for Sm (Co, Cu), alloys containing 0 to 75 at % copper. The optimum area for magnetic values was shifted toward the samariumpoor side from the line connecting the compound SmCos with SmCu5. Differential thermal analysis (DTA) revealed that the endothermic reaction temperatures were around 920°C and scarcely varied in alloys containing from 16 to 66 at copper. This suggests that the phase transformation may occur at this temperature regardless of different copper contents. In Sm(Co, Cu)5 alloys a single Curie point (T.) was observed on rapid heating from the as-cast condition, and two points on slow cooling after heating at 1000°C for 30 min. One of the Curie points belongs to a SmCo5 structure type and the other to a compound isostructural with Sm2Co17. From the results of DTA and measurements of Tc and magnetic values, a hypothetical Sm-Co-Cu ternary phase diagram is proposed, in which the alloys initially containing 24 to 40 at % copper may decompose spinodally. (Received June 5, 1972)
High-speed photorefractive keratectomy with femtosecond ultraviolet pulses

Abstract. Femtosecond near-infrared lasers are widely used for a number of ophthalmic procedures, with flap cutting in the laser-assisted in situ keratomileusis (LASIK) surgery being the most frequent one. At the same time, lasers of this type, equipped with harmonic generators, have been shown to deliver enough ultraviolet (UV) power for the second stage of the LASIK procedure, the stromal ablation. However, the speed of the ablation reported so far was well below the currently accepted standards. Our purpose was to perform high-speed photorefractive keratectomy (PRK) with femtosecond UV pulses in rabbits and to evaluate its predictability, reproducibility and healing response. The laser source delivered femtosecond 206 nm pulses with a repetition rate of 50 kHz and an average power of 400 mW. Transepithelial PRK was performed using two different ablation protocols, to a total depth of 110 and 150 μm. The surface temperature was monitored during ablation; haze dynamics and histological samples were evaluated to assess outcomes of the PRK procedure. For comparison, analogous excimer ablation was performed. Increase of the ablation speed up to 1.6 s/diopter for a 6 mm optical zone using femtosecond UV pulses did not significantly impact the healing process.
Microeconomic relationships between and among fishers and traders influence the ability to respond to social-ecological changes in a small-scale fishery

Understanding the cross-scale nature of how natural resource trading links to local extraction patterns remains a topic of great relevance to stewardship and sustainable use of ecological systems. Microeconomic influences on a society’s pattern of small-scale natural resources utilization can exacerbate resource overuse, especially under increased population pressure. In many rural communities that are based on a limited diversity of resource industries, quantifying the response of extractors and traders to market and environmental fluctuations is critical to understanding management constraints. We examine the fishing practices of a small lake in Uganda, East Africa, from the dual perspectives of the traders and the fishers using a Bayesian Belief Network approach based on detailed interview surveys. Fishers in this small lake target Nile perch (Lates niloticus) and Nile tilapia (Oreochromis niloticus), two fish species of high commercial and food security significance in East Africa. We combined data on financial, social, and ecological systems to understand how aspects of trading quantitatively relate to fish extraction patterns in Lake Nabugabo Uganda. Importantly, we find that the patron-client type relationships generate incentives to extract specific fish, whereas “freelancer” independent fishers are able to create responsive and flexible extraction practices that match market and environmental fluctuations. Management of fishing administered by local Beach Management Units will likely have a higher probability of success when in synchrony with trading relationships and ecological dynamics. We use this study in Uganda to reflect on methodological challenges and opportunities of combining multiple types of data sets for cross-scale analysis of social-ecological system dynamics.
Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging

Significance The world’s population is growing older, and senescence of the immune system is a fundamental factor underlying morbidity and mortality. We report a direct molecular characterization of the effects of aging on the adaptive immune system by high-throughput sequencing of antibody transcripts in the peripheral blood of humans. Using a phylogenetic approach to quantify dissimilarity, we compared the immunoglobulin repertoires of young and elderly individuals at baseline and during a well-defined immunogenic perturbation in the form of influenza vaccination; we also studied the long-term effects of chronic infection. Our work reveals previously unappreciated signatures of immune senescence that may find diagnostic use and guide approaches for improving elderly patients’ antibody responses. The elderly have reduced humoral immunity, as manifested by increased susceptibility to infections and impaired vaccine responses. To investigate the effects of aging on B-cell receptor (BCR) repertoire evolution during an immunological challenge, we used a phylogenetic distance metric to analyze Ig heavy-chain transcript sequences in both young and elderly individuals before and after influenza vaccination. We determined that BCR repertoires become increasingly specialized over a span of decades, but less plastic. In 50% of the elderly individuals, a large space in the repertoire was occupied by a small number of recall lineages that did not decline during vaccine response and contained hypermutated IgD+ B cells. Relative to their younger counterparts, older subjects demonstrated a contracted naive repertoire and diminished intralineage diversification, signifying a reduced substrate for mounting novel responses and decreased fine-tuning of BCR specificities by somatic hypermutation. Furthermore, a larger proportion of the repertoire exhibited premature stop codons in some elderly subjects, indicating that aging may negatively affect the ability of B cells to discriminate between functional and nonfunctional receptors. Finally, we observed a decreased incidence of radical mutations compared with conservative mutations in elderly subjects’ vaccine responses, which suggests that accumulating original antigenic sin may be limiting the accessible space for paratope evolution. Our findings shed light on the complex interplay of environmental and gerontological factors affecting immune senescence, and provide direct molecular characterization of the effects of senescence on the immune repertoire.
Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing

Blood is a dense suspension of soft non-Brownian cells of unique importance. Physiological blood flow involves complex interactions of blood cells with each other and with the environment due to the combined effects of varying cell concentration, cell morphology, cell rheology, and confinement. We analyze these interactions using computational morphological image analysis and machine learning algorithms to quantify the non-equilibrium fluctuations of cellular velocities in a minimal, quasi-two-dimensional microfluidic setting that enables high-resolution spatio-temporal measurements of blood cell flow. In particular, we measure the effective hydrodynamic diffusivity of blood cells and analyze its relationship to macroscopic properties such as bulk flow velocity and density. We also use the effective suspension temperature to distinguish the flow of normal red blood cells and pathological sickled red blood cells and suggest that this temperature may help to characterize the propensity for stasis in Virchow's Triad of blood clotting and thrombosis.
Doubling the Performance of Python/NumPy with less than 100 SLOC

—A very simple, and outside NumPy, commonly used trick of buffer-reuse is introduced to the NumPy library to speed up the performance of scientiﬁc applications in Python/NumPy. The implementation, which we name software victim-caching, is very simple. The code itself consists of less than 100 lines of code, and took less than one day to add to NumPy, though it should be noted that the programmer was very familiar with the inner workings of NumPy. The result is an improvement of as much as 2.29 times speedup, on average 1.32 times speedup across a benchmark suite of 15 applications, and at no time did the modiﬁcation perform worse than unmodiﬁed NumPy.
Tibial dyschondroplasia is closely related to suppression of expression of hypoxia-inducible factors 1α, 2α, and 3α in chickens

Tibial dyschondroplasia (TD) cases has not been reported in Tibetan chickens (TBCs), but it is commonly seen in commercial broilers characterized by lameness. The underlying mechanism remains unclear. Hypoxia-inducible factors (HIFs) are important regulators of cellular adaptation to hypoxic conditions. In this study, we investigated the role of HIF-1α, -2α, and -3α in hypoxia and thiram-induced TD and their effect on tibial growth plate development in Arbor Acres chickens (AACs) and TBCs. RNA and protein expression levels of HIF-1α, -2α, and -3α were determined by using quantitative reverse transcriptase polymerase chain reaction and western blotting analyses, respectively. Interestingly, the results showed that HIF-1α, -2α, and -3α expressions in the tibial growth plate of TBCs were upregulated by hypoxia and the change was more significant in TBCs than in AACs. However, these factors were downregulated in thiram-induced TD. To further clarify the effect of thiram on tibial growth plate in commercial broilers, AACs were observed to exhibit more pronounced changes in their growth plate that that in TBCs. Taken together, these results demonstrate that HIF-1α, -2α, and -3α may be important in tibial growth plate development and in the prevention of TD. The present study contributes novel insights on a therapeutic target for poultry TD.
Fractography and Damage Analysis of Carbon/Epoxy Composites Under Static and Dynamic Loading at Elevated Temperatures

This paper presents the microstructural and fractographic analysis of damage in carbon/epoxy composites after static and fatigue strength (shear) tests at elevated temperature. The microstructural tests and fractographic analysis confirmed the complexity of degradation process and degradation mechanisms in composite structure. Multiple cracks, delaminations and interface degradation between fibre and matrix have been observed. The fracture analysis indicate the occurrence of characteristic failure area: matrix river lines, matrix rollers, fractures and reinforcing fibres imprints. The interface, except of the type of components and their features, is the principal factor determining the properties of composite material. The quality of the bonding between the reinforcing phase and matrix, mechanism of composite cracking as a whole as well as cracks of individual components are directly affected by the interface.
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.

Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific "transcriptional noise. " Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.
Integration of nitrogen dynamics into the Noah-MP land surface model v1.1 for climate and environmental predictions

Abstract. Climate and terrestrial biosphere models consider nitrogen an important factor in limiting plant carbon uptake, while operational environmental models view nitrogen as the leading pollutant causing eutrophication in water bodies. The community Noah land surface model with multi-parameterization options (Noah-MP) is unique in that it is the next-generation land surface model for the Weather Research and Forecasting meteorological model and for the operational weather/climate models in the National Centers for Environmental Prediction. In this study, we add a capability to Noah-MP to simulate nitrogen dynamics by coupling the Fixation and Uptake of Nitrogen (FUN) plant model and the Soil and Water Assessment Tool (SWAT) soil nitrogen dynamics. This model development incorporates FUN's state-of-the-art concept of carbon cost theory and SWAT's strength in representing the impacts of agricultural management on the nitrogen cycle. Parameterizations for direct root and mycorrhizal-associated nitrogen uptake, leaf retranslocation, and symbiotic biological nitrogen fixation are employed from FUN, while parameterizations for nitrogen mineralization, nitrification, immobilization, volatilization, atmospheric deposition, and leaching are based on SWAT. The coupled model is then evaluated at the Kellogg Biological Station – a Long Term Ecological Research site within the US Corn Belt. Results show that the model performs well in capturing the major nitrogen state/flux variables (e.g., soil nitrate and nitrate leaching). Furthermore, the addition of nitrogen dynamics improves the modeling of net primary productivity and evapotranspiration. The model improvement is expected to advance the capability of Noah-MP to simultaneously predict weather and water quality in fully coupled Earth system models.
The role of gastric mucosal histamine in acid secretion and experimentally induced lesions in the rat.

The role played by histamine from enterochromaffin-like (ECL) cells and mast cells in gastric acid secretion and in the development of ethanol-induced gastric lesions was studied in the rat. This was done by examining the effects of inhibition of the histamine-producing enzyme histidine decarboxylase (HDC) with alpha-fluoromethylhistidine (alpha-FMH) and the effects of degranulation of the mucosal mast cells with dexamethasone. A single dose of alpha-FMH (50 mg/kg p.o.) inhibited the HDC activity by 94% but did not affect histamine levels in the gastric mucosa 2 h after dose. Repeated treatment resulted in an almost complete inhibition of HDC activity and in a reduction of histamine levels by 75%. Pentagastrin failed to stimulate acid secretion after 4 days treatment with alpha-FMH, whereas the acid response to histamine was unaffected in chronic gastric fistula rats. Ethanol failed to induce gastric lesions in rats pretreated for 4 days with dexamethasone whereas 4 days pretreatment with alpha-FMH did not influence ethanol-induced lesion formation. The present results show that histamine synthesis is required for pentagastrin-stimulated gastric acid secretion and that mucosal mast-cell histamine plays a role in the development of ethanol-induced gastric lesions.
The Relations between Area Functions and the Acoustic Signal

Abstract To derive speech wave data from area function specifications and the reverse, to predict the area function from the speech wave, are fundamental problems of acoustic theory of speech production. Deviations from ideal resonator theory in terms of vocal tract boundary conditions and source filter interactions are discussed. Perturbation theory is related to special problems of male-female vocal tract scaling. Shortcomings of the inverse transforms are discussed. Merits of lossy transmission line theory over standard linear prediction procedures are emphasized. The use of bandwidths for removing ambiguities is illustrated in simple models. A limited amount of bandwidth data supplementing formant frequency data and model related vocal tract constraints appears to be optimal.
Análise térmica da massa de pão francês durante os processos de congelamento e descongelamento: otimização do uso de aditivos.

Bread produced from frozen dough has been improved due to technological advances and formulation, however it still presents problems like long proofing, low specific volume, varied texture and performance. The effect of freezing can be minimized by use of additives and adequate ingredients. The mechanism of dough strengthening due to use of additives, such as emulsifiers, is not fully understood. Thermal analysis is a useful tool for food research, development and quality control, because it provides information on food structural changes during thermal treatment. The goal of this research is to study the influence of additives in bread making on French bread dough after a freeze-thaw cycles. The experimental part consists of four parts: in the first, different formulations were produced with the components calcium stearoyl-2-lactylate (CSL), polysorbate 80 (PS80) and vegetable shortening (VGH); in the second, a mixture design with three components (CSL, PS80 and diacetyl tartaric esters of mono and digliceride – DATEM) was made; in the third, influence of ascorbic acid was studied on rheological measurement and events determined by differential scanning calorimetry (DSC) to optimize the use of additives on frozen dough. Thermal analysis was adequate for the freeze-thaw events, however not for the heating events. Resistance to extension and dough extensibility were influenced by storage time. In the fourth part, French breads from frozen dough were produced with the mixture (0,3 % of PS80 and 0,2 % of DATEM in flour basis) and two levels of ascorbic acid. Specific volume, texture profile, water content, gas production and mass tolerance during proofing were determined. Breads made with ascorbic acid addition presented a higher specific volume and lower values for texture profile (firmness, springiness, cohesiveness and chewiness).
Prediction of Lung Motion From Four-Dimensional Computer Tomography (4DCT) Images Using Bayesian Registration and Trajectory Modelling

Respiratory motion causes difficulty in locating tumours in the thorax and upper abdomen for image-guided radiotherapy. Precisely predicting the respiratory-induced organ motion is still a challenging problem at present. In this paper, to predict the motion of lungs in a respiratory cycle, we propose a novel method comprising Bayesian registration and trajectory modelling based on cine four-dimensional computer tomography (4DCT) images. Specifically, we take the CT image captured at the end-inhale phase as the source image and those captured at other phases as the moving images. We then align the source image to each moving-phase image to generate the displacement fields using the Bayesian registration method. The lung-motion trajectory is then modelled based on a continuous time-related displacement field by linking the displacement fields at discrete phases. The results indicate that any point in the lungs at any given time is accurately predicted using the proposed method, which provides an alternative method of estimating the lung and tumour motions for radiation therapy.
A Fast Channel Assignment Scheme for Emergency Handling in Wireless Body Area Networks

Ubiquitous healthcare is a promising technology that has attracted significant attention in recent years; this has led to the realization of wireless body area networks (WBANs). For designing a robust WBAN system, the WBAN has to solve the drawbacks of wireless technology. Also, a WBAN has to support immediate, reliable data transmission for medical services during emergencies. Hence, this study proposes a new MAC superframe structure that can handle emergencies by delivering strongly correlated regular data to a caretaker, within a certain time threshold. Simulation results demonstrate that the proposed MAC protocol achieves low latency and high throughput.