Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Storage Duration and Temperature on the Chemical Composition, Microorganism Density, and In vitro Rumen Fermentation of Wet Brewers Grains

This study aimed to investigate the effects of storage duration and temperature on the characteristics of wet brewers grains (WBG) as feeds for ruminant animals. Four storage temperatures (5°C, 15°C, 25°C, and 35°C) and four durations (0, 1, 2, and 3 d) were arranged in a 4×4 factorial design. Surface spoilage, chemical composition and microorganism density were analyzed. An in vitro gas test was also conducted to determine the pH, ammonia-nitrogen and volatile fatty acid (VFA) concentrations after 24 h incubation. Surface spoilage was apparent at higher temperatures such as 25°C and 35°C. Nutrients contents decreased concomitantly with prolonged storage times (p<0.01) and increasing temperatures (p<0.01). The amount of yeast and mold increased (p<0.05) with increasing storage times and temperatures. As storage temperature increased, gas production, in vitro disappearance of organic matter, pH, ammonia nitrogen and total VFA from the WBG in the rumen decreased (p<0.01). Our results indicate that lower storage temperature promotes longer beneficial use period. However, when storage temperature exceeds 35°C, WBG should be used within a day to prevent impairment of rumen fermentation in the subtropics such as Southeast China, where the temperature is typically above 35°C during summer.
Interventions to Reduce Behavioral Problems in Children With Cerebral Palsy: An RCT

OBJECTIVE: To test Stepping Stones Triple P (SSTP) and Acceptance and Commitment Therapy (ACT) in a trial targeting behavioral problems in children with cerebral palsy (CP). METHODS: Sixty-seven parents (97.0% mothers; mean age 38.7 ± 7.1 years) of children (64.2% boys; mean age 5.3 ± 3.0 years) with CP (Gross Motor Function Classification System = 15, 22%; II = 18, 27%; III =12, 18%; IV = 18, 27%; V = 4, 6%) participated and were randomly assigned to SSTP, SSTP + ACT, or waitlist. Primary outcomes were behavioral and emotional problems (Eyberg Child Behavior Inventory [ECBI], Strengths and Difficulties Questionnaire [SDQ]) and parenting style (Parenting Scale [PS]) at postintervention and 6-month follow-up. RESULTS: SSTP with ACT was associated with decreased behavioral problems (ECBI Intensity mean difference [MD] = 24.12, confidence interval [CI] 10.22 to 38.03, P = .003; ECBI problem MD = 8.30, CI 4.63 to 11.97, P < .0001) including hyperactivity (SDQ MD = 1.66, CI 0.55 to 2.77, P = .004), as well as decreased parental overreactivity (PS MD = 0.60, CI 0.16 to 1.04, P = .008) and verbosity (PS MD = 0.68, CI 0.17 to 1.20, P = .01). SSTP alone was associated with decreased behavioral problems (ECBI problems MD = 6.04, CI 2.20 to 9.89, P = .003) and emotional symptoms (SDQ MD = 1.33, CI 0.45 to 2.21, P = .004). Decreases in behavioral and emotional problems were maintained at follow-up. CONCLUSIONS: SSTP is an effective intervention for behavioral problems in children with CP. ACT delivers additive benefits.
Incidence of Pleural Recurrence after Computed Tomography-Guided Needle Biopsy in Stage I Lung Cancer

Objective A risk of tumor seeding after percutaneous needle biopsy has been reported in various organs, including the lung. This study retrospectively evaluated the proportion of ipsilateral pleural recurrence after computed tomography-guided needle biopsy (CTNB) in p-stage I lung cancer patients. Methods Of the 321 patients diagnosed with p-stage I lung cancer, 124 underwent CTNB before surgery, while 197 underwent non-CTNB procedures, including bronchoscopic biopsy in 188 patients and thoracoscopic wedge resection in 9. These patients were retrospectively analyzed. Results While the tumor size was significantly larger in the non-CTNB group (25±9 mm) in comparison to the CTNB group (19±9 mm) (p<0.001), percentage of pleural, vascular, or lymphatic invasions were comparable between the two groups. Eight patients developed ipsilateral pleural recurrences, one (1%) in the CTNB group, and 7 (4%) in the non-CTNB group. Of these, 3 patients developed pleural recurrence only at first, 1 (1%) in the CTNB group, and 2 (1%) in the non-CTNB group. The differences in the proportions of these pleural recurrences between the 2 groups were not significant. Subgroup analyses by baseline characteristics such as tumor size, pT stage, or microscopic pleural invasion, showed that proportions of pleural recurrences in CTNB group were not high compared with non-CTNB group in each subgroup. Analysis of progression-free survival showed that recurrences in CTNB were not high compared with non-CTNB. Conclusions The pleural recurrence was not significantly increased after CTNB in p-stage I lung cancer patients in this particular study.
EXPERIMENTAL STUDIES OF PHOTOCATHODE RF GUN WITH LASER PULSE SHAPING

A technique of laser pulse shaping was developed for low-emittance electron beam generation in a photocathode RF gun. The emittance growth due to space charge and RF effects in the RF gun was experimentally investigated with square and gaussian temporal laser pulse shapes. It is found that the square pulse shaping is a useful tool for both the reduction of nonlinear space charge force and the correction of the linear space charge effect. An optimal normalized rms emittance of 1.2 πmmmrad at 1 nC was obtained by a square temporal laser pulse shape with pulse length of 9 ps FWHM.
Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons

Thousands of tandem alternative splice sites (TASS) give rise to mRNA insertion/deletion variants with small size differences. Recent work has concentrated on the question of biological relevance in general, and the physiological regulation of TASS in particular. We have quantitatively studied 11 representative TASS cases in comparison to one mutually exclusive exon case and two cassette exons (CEs) using a panel of human and mouse tissues, as well as cultured cell lines. Tissues show small but significant differences in TASS isoform ratios, with a variance 4- to 20-fold lower than seen for CEs. Remarkably, in cultured cells, all studied alternative splicing (AS) cases showed a cell-density-dependent shift of isoform ratios with similar time series profiles. A respective genome-wide co-regulation of TASS splicing was shown by next-generation mRNA sequencing data. Moreover, data from human and mouse organs indicate that this co-regulation of TASS occurs in vivo, with brain showing the strongest difference to other organs. Together, the results indicate a physiological AS regulation mechanism that functions almost independently from the splice site context and sequence.
The Origin of the Vertebrate Jaw: Neoclassical Ideas Versus Newer, Development-Based Ideas

Abstract Here I consider ways to test two hypotheses of the origin of jawed vertebrates: my neoclassical hypothesis, which derived from comparative morphology; and the heterotopic hypothesis, which derives from modern developmental findings. The heterotopic hypothesis, unlike the neoclassical hypothesis, says that major developmental changes had to occur before the upper jaws could evolve: a caudal shift in the expression domains of genes that pattern oral structures; and the loss of ancestral, lamprey-like upper lips. To test whether these did occur, I propose studies on the development of chondrichthyans (sharks and chimaeroid ratfishes), an understudied group that is likely to retain primitive features of the jaw region. The heterotopic hypothesis says no gnathostome retains the upper lip that is so prominent in larval lampreys, yet the neoclassical hypothesis identified such lips in sharks and ratfishes, and it predicts that their lip-skeleton likewise develops from premandibular neural crest. The development and innervation of upper-lip muscles in lampreys and chimaeroids can also be compared. The proposed studies can determine if the upper lips of chondrichthyans and lampreys are homologous (which would support the neoclassical hypothesis), or homoplasious (which would support the heterotopic hypothesis). Also, I argue that the evolution of the upper jaws (as lateral structures) was not linked to a nasohypophyseal complex (which is a median structure), although such a link is claimed by the heterotopic hypothesis. Finally, I update the neoclassical hypothesis to address recent evidence that the trabeculae of the lamprey skull are not homologous to the trabeculae cranii of gnathostomes.
Stochastic Nature of the Casting Solidification Displayed by Micro-Modelling and Cellular Automata Method

Some aspects of stochastic nature of the solidification processes are described. Firstly, the influence of the random grains nucleation on the cooling curves repeatability in the thin wall casting is presented. Secondly, the foundations of an average shape prediction for geometry of ele¬mentary diffusion field (concept of the Averaged Voronoi Polyhedron, AVP) are shown for the mi¬cro-modelling of the diffusion limited growth. Stochastic nature of the grains nucleation and growth is taken into account in the solidification modelling based on the Cellular Automaton technique (CA).
Imaging of central nervous system viral diseases

Viral infections of the central nervous system (CNS) are commonly encountered and there has been continued emergence of new neurotropic viruses which are being frequently recognized. These may present clinically as encephalitis, meningitis, encephalomyelitis, and encephalomyeloradiculitis. The clinical manifestations are usually nonspecific and diagnosis is usually based on the laboratory investigations. Imaging plays a role in its early detection and at times suggests the specific diagnosis that may help in early institution of appropriate therapy. In this review, we summarize the pathology, clinical, and imaging features of the common viral infections that affect the CNS. J. Magn. Reson. Imaging 2012;35:477‐491. © 2012 Wiley Periodicals, Inc.
Parallel and distributed graph cuts by dual decomposition

Graph cuts methods are at the core of many state-of-the-art algorithms in computer vision due to their efficiency in computing globally optimal solutions. In this paper, we solve the maximum flow/minimum cut problem in parallel by splitting the graph into multiple parts and hence, further increase the computational efficacy of graph cuts. Optimality of the solution is guaranteed by dual decomposition, or more specifically, the solutions to the subproblems are constrained to be equal on the overlap with dual variables. We demonstrate that our approach both allows (i) faster processing on multi-core computers and (ii) the capability to handle larger problems by splitting the graph across multiple computers on a distributed network. Even though our approach does not give a theoretical guarantee of speedup, an extensive empirical evaluation on several applications with many different data sets consistently shows good performance. An open source implementation of the dual decomposition method is also made publicly available.
The Pathogenesis, Clinical Implications, and Treatment of Intestinal Hyperpermeability

Normally, the gastrointestinal epithelium provides a semi-permeable barrier which allows nutrients to be absorbed while preventing larger, potentially toxic, antigenic, or pathogenic molecules or organisms from crossing into the bloodstream. Pathogenicallyincreased intestinal permeability predisposes the individual to diffusion of antigenic food molecules and translocation of bacteria and/or yeast from the gut to extra-intestinal sites, including mesenteric lymph nodes, liver, spleen, and systemic circulation. This can be secondary to drugs, microbial overgrowth, radiation, stress, alcohol intake, enteral/parenteral nutrition, or injury. Increased intestinal permeability occurs commonly with diseases including inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis, asthma, eczema, food allergies, alcoholism, trauma, and surgery. Glutamine, phosphatidylcholine, flavonoids, soluble fiber, and fish oil, as well as probiotic organisms, including Lactobacilli and Saccharomyces boulardii can assist in correcting this abnormal permeability.
HAMR: high-throughput annotation of modified ribonucleotides

When converted to cDNA in the course of RNA sequencing, modified RNA nucleotides can produce sequence patterns that are distinguishable from simple base-calling errors. The authors developed a method, HAMR, that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications.
Modeling of River Water Temperatures using Feed-forward Artificial Neural Networks

Water temperature influences most physical, chemical and biological processes of the river environment. It plays an important role in the distribution of fishes and on the growth rates of many aquatic organisms. It is therefore important to develop water temperature models in order to effectively manage aquatic habitats, to study the thermal regime of rivers and to have effective tools for environmental impact studies. The objective of the present study was to develop a water temperature model based on artificial neural networks (ANN) for two thermally different watercourses. The ANN model performed best in summer and autumn and showed a poorer (but still good) performance in spring. The many advantages of ANN models are their simplicity, low data requirements, their capability of modelling long-term series as well as have an overall
Chronobiological aspects of food intake and metabolism and their relevance on energy balance and weight regulation

Overweight and obesity are the result of a chronic positive energy balance, and therefore the only effective therapies are a diet which, on the long term, provides lower calories than the daily expended energy and exercise. Because nearly every physiological and biochemical function of the body shows circadian variations it can be suggested that also different chronobiological aspects of food intake, like time of day, meal frequency and regularity, and also circadian desynchronizations like in shift work may affect energy metabolism and weight regulation. The aim of this review is therefore to summarize and discuss studies that have addressed these issues in the past and to also provide an overview about circadian variations of selected aspects of metabolism, gut physiology and also factors that may influence overall energy regulation. The results show that a chronic desynchronization of the circadian system like in shift work and also sleep deprivation can favour the development of obesity. Also, regarding energy balance, a higher meal frequency and regular eating pattern seem to be more advantageous than taking the meals irregularly and seldom. Additional studies are required to conclude whether time of day‐dependent food intake significantly influences weight regulation in humans.
Targeted Restoration of Down-regulated DAPK2 Tumor Suppressor Activity Induces Apoptosis in Hodgkin Lymphoma Cells

Death-associated protein kinase 2 (DAPK2) is a calcium/calmodulin-regulated proapoptotic serine/threonine kinase that acts as a tumor suppressor. Here we show that DAPK2 is down-regulated in Hodgkin lymphoma-derived tumor cell lines and that promoter-region hypermethylation is one mechanism for DAPK2 inactivation. To determine whether selective reconstitution of DAPK2 catalytic activity in these cells could induce apoptosis, we created a fusion protein comprising a human CD30 ligand conjugated to a human DAPK2 calmodulin-deletion mutant. Thus, recombinant immunokinase DAPK2′-CD30L has a constitutive kinase activity with enhanced proapoptotic function. We show that this immunokinase fusion protein inhibits cell proliferation and induces apoptotic cell death specifically in CD30+/DAPK2-negative tumor cell lines. This proof-of–concept study provides the first demonstration of therapeutic strategies based on the restoration of a defective, tumor-suppressing kinase activity by a novel class of recombinant immunotherapeutics.
Twenty-year trends in coronary risk factors in north Karelia and in other areas of Finland.

BACKGROUND The North Karelia Project, a major demonstration programme for coronary heart disease (CHD) prevention, began in the eastern province of North Karelia in Finland in 1972. A number of other national CHD prevention activities have also been undertaken particularly since 1977. In the 1980s, a national strategy was developed for CHD prevention. This paper reports the 20-year changes in risk factors in North Karelia and in the original reference area of the project and the 10-year changes in a third area in southwestern Finland. METHODS The results are based on comparable surveys of cross-sectional population samples, aged 30-59 years, every fifth year since 1972. RESULTS During the first 5 years total cholesterol and blood pressure fell more in North Karelia than in the reference area, but subsequently changes have been about the same in both areas. The decline levelled off between the 1982 and 1987 surveys. This resulted in new nationwide preventive activities and during the last 5 years major declines in both serum total cholesterol and blood pressure have been observed. Smoking reduced more during the first 10 years in North Karelia than in Kuopio province. During the last 10 years a small decline has been observed in both areas. No change in smoking has occurred in southwestern Finland in the last 10 years. CONCLUSIONS A major decline in cardiovascular disease risk factors has been observed in the last 20 years in Finland. This decline was associated with the launch of the national demonstration project in North Karelia in the 1970s and with subsequent major national activities thereafter.
Spitzer Observations of MAMBO Galaxies: Weeding Out Active Nuclei in Starbursting Protoellipticals

We present 3.6-24 μm Spitzer observations of an unbiased sample of nine luminous, dusty galaxies selected at 1200 μm by MAMBO on the IRAM 30 m telescope, a population akin to the well-known submillimeter or SCUBA galaxies (hereafter SMGs). Owing to the coarse resolution of submillimeter/millimeter cameras, SMGs have traditionally been difficult to identify at other wavelengths. We compare our multiwavelength catalogs to show that the overlap between 24 and 1200 μm must be close to complete at these flux levels. We find that all (4/4) of the most secure ≥4 σ SMGs have ≥4 σ counterparts at 1.4 GHz, while the fraction drops to 7/9 using all ≥3 σ SMGs. We show that combining mid-infrared (MIR) and marginal (≥3 σ) radio detections provides plausible identifications in the remaining cases, enabling us to identify the complete sample. Accretion onto an obscured central engine is betrayed by the shape of the MIR continuum emission for several sources, confirming Spitzer's potential to weed out active galaxies. We demonstrate the power of an S24 μm/S8 μm versus S8 μm/S4.5 μm color-color plot as a diagnostic for this purpose. However, we conclude that the majority (∼75%) of SMGs have rest-frame mid/far-IR spectral energy distributions commensurate with obscured starbursts. Sensitive 24 μm observations are clearly a useful route to identify and characterize reliable counterparts to high-redshift far-IR-bright galaxies, complementing what is possible via deep radio imaging.
Global and Specific Translational Regulation in the Genomic Response of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source

ABSTRACT The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs. Features of the program included a transient reduction in global translational activity and a severe decrease in polysome size of transcripts encoding ribosomal proteins. While the overall translation initiation of newly synthesized and preexisting mRNAs was generally repressed after the carbon source shift, the mRNA encoded by YPL250C was an exception in that it selectively mobilized into polysomes, although its relative abundance remained unchanged. In addition, splicing of HAC1transcripts, which has previously been reported to occur during accumulation of unfolded proteins in the endoplasmic reticulum, was observed after the carbon shift. This finding suggests that the nonconventional splicing complex, composed of the kinase-endonuclease Ire1p and the tRNA ligase Rlg1p, was activated. While splicedHAC1 transcripts mobilized into polysomes, the vast majority of unspliced HAC1 RNA accumulated in nonpolysomal fractions before and after the carbon source shift, indicating that translation of unspliced HAC1 RNA is blocked at the translation initiation step, in addition to the previously reported elongation step. These findings reveal that S. cerevisiaereacts to the carbon source shift with a remarkable variety of responses, including translational regulation of specific mRNAs and activation of specific enzymes involved in a nonconventional splicing mechanism.
Super-rigidity for holomorphic mappings between hyperquadrics with positive signature

We study local holomorphic mappings sending a piece of a real hyperquadric in a complex space into a hyperquadric in another complex space of possibly larger dimension. We show that these mappings possess strong super-rigidity properties when the hyperquadrics have positive signatures. These results are applied in the context of holomorphic mappings between classical domains in complex projective spaces of different dimensions.