Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Alternative Splicing by Reversible Protein Phosphorylation*

The vast majority of human protein-coding genes are subject to alternative splicing, which allows the generation of more than one protein isoform from a single gene. Cells can change alternative splicing patterns in response to a signal, which creates protein variants with different biological properties. The selection of alternative splice sites is governed by the dynamic formation of protein complexes on the processed pre-mRNA. A unique set of these splicing regulatory proteins assembles on different pre-mRNAs, generating a “splicing” or “messenger ribonucleoprotein code” that determines exon recognition. By influencing protein/protein and protein/RNA interactions, reversible protein phosphorylation modulates the assembly of regulatory proteins on pre-mRNA and therefore contributes to the splicing code. Studies of the serine/arginine-rich protein class of regulators identified different kinases and protein phosphatase 1 as the molecules that control reversible phosphorylation, which controls not only splice site selection, but also the localization of serine/arginine-rich proteins and mRNA export. The involvement of protein phosphatase 1 explains why second messengers like cAMP and ceramide that control the activity of this phosphatase influence alternative splicing. The emerging mechanistic links between splicing regulatory proteins and known signal transduction pathways now allow in detail the understanding how cellular signals modulate gene expression by influencing alternative splicing. This knowledge can be applied to human diseases that are caused by the selection of wrong splice sites.
Genetic Variation and Combining Ability Analysis of Bruising Sensitivity in Agaricus bisporus

Advanced button mushroom cultivars that are less sensitive to mechanical bruising are required by the mushroom industry, where automated harvesting still cannot be used for the fresh mushroom market. The genetic variation in bruising sensitivity (BS) of Agaricus bisporus was studied through an incomplete set of diallel crosses to get insight in the heritability of BS and the combining ability of the parental lines used and, in this way, to estimate their breeding value. To this end nineteen homokaryotic lines recovered from wild strains and cultivars were inter-crossed in a diallel scheme. Fifty-one successful hybrids were grown under controlled conditions, and the BS of these hybrids was assessed. BS was shown to be a trait with a very high heritability. The results also showed that brown hybrids were generally less sensitive to bruising than white hybrids. The diallel scheme allowed to estimate the general combining ability (GCA) for each homokaryotic parental line and to estimate the specific combining ability (SCA) of each hybrid. The line with the lowest GCA is seen as the most attractive donor for improving resistance to bruising. The line gave rise to hybrids sensitive to bruising having the highest GCA value. The highest negative SCA possibly indicates heterosis effects for resistance to bruising. This study provides a foundation for estimating breeding value of parental lines to further study the genetic factors underlying bruising sensitivity and other quality-related traits, and to select potential parental lines for further heterosis breeding. The approach of studying combining ability in a diallel scheme was used for the first time in button mushroom breeding.
Nomenclature of human platelet alloantigens: a problem with the HPA system?

HE PAST SEVERAL YEARS have witnessed the elu- cidation of the molecular basis of a number of clini- cally relevant human platelet alloantigen systems. It would appear from the data collected from a number of different laboratories that the existence ofall ofthe offending epitopes seems to be due to the presence of single amino acid substi- tutions within the polypeptide chain of the glycoprotein (GP) that bears the alloantigenic epitope. ”’ Biochemical and immunochemical characterization of allele-specific re- combinant forms of these platelet membrane GPs has shown, in those
Microarchitecture-based introspection: a technique for transient-fault tolerance in microprocessors

The increasing transient fault rate necessitates on-chip fault tolerance techniques in future processors. The speed gap between the processor and the memory is also increasing, causing the processor to stay idle for hundreds of cycles while waiting for a long-latency cache miss to be serviced. Even in the presence of aggressive prefetching techniques, future processors are expected to waste significant processing bandwidth waiting for main memory. This paper proposes microarchitecture-based introspection (MBI), a transient-fault detection technique, which utilizes the wasted processing bandwidth during long-latency cache misses for redundant execution of the instruction stream. MBI has modest hardware cost, requires minimal modifications to the existing microarchitecture, and is particularly well suited for memory-intensive applications. Our evaluation reveals that the time redundancy of MBI results in an average IPC reduction of only 7.1 %for memory-intensive benchmarks in the SPEC CPU2000 suite. The average IPC reduction for the entire suite is 14.5%.
A compact wideband hybrid dielectric resonator antenna

A novel wideband hybrid dielectric resonator antenna structure comprises a rectangular dielectric resonator (DR) and a coplanar waveguide (CPW) inductive slot is proposed. In this configuration, the CPW inductive slot simultaneously acts as an effective radiator and the feeding structure of the DR. Dual resonances of the two radiators are merged to extend the antenna's bandwidth. A parametric study is performed to optimize the antenna performance and a prototype for 5-GHz WLAN application has been built and tested.
Refinements of the Radiographic Cadaver Injection Technique for Investigating Minute Lymphatic Vessels

Background: The authors previously reported a new technique with which to delineate the lymphatic vessels, using hydrogen peroxide to identify them and a lead oxide suspension to demonstrate them on radiographs. This technique provided excellent studies of the lymph vessels in human cadavers, but there was still room for improvement. Methods: Lymph collecting vessels run superficially in some regions, where they may be damaged while the surgeon is attempting to find them. Vessels smaller than 0.3 mm in diameter could not be cannulated with a 30-gauge needle, which was the smallest the authors had available, and the lead oxide suspension often blocked this cannula. The authors also encountered problems holding the cannula steady. Results: The authors solved these problems by using a mixture of hydrogen peroxide and ink to better identify the lymphatics, an extruded glass tube instead of a metal needle to cannulate them, an agate pestle and mortar to grind the lead oxide into finer particles, powdered milk to suspend the lead oxide, and a micromanipulator to facilitate accurate and steady cannulation of the vessels. Conclusion: This study developed these modifications to focus on tributaries of the collecting lymphatic channels that are smaller than 0.3 mm in diameter.
High-speed plastic optical fibers and amplifiers

Recent progress of the graded-index polymer optical fiber (GI POF) and polymer optical fiber amplifier (POFA) are reviewed. Because the low attenuation of light transmission in the perfluorinated (PF) polymer base GI POF enables 500 to 1000 m transmission, more accurate analysis is required in the refractive index profile to realize the order of giga bit transmission. Furthermore, recent improvement of the thermal stability of the GI POF is introduced. We clarified that the stability of the refractive index profile and the attenuation under high temperature and high humidity atmosphere can be improved by selecting the suitable dopant material. We demonstrated that organic dye-doped POFA cover a wide spectral range in the visible with a best observed gain of 37 dB in a Rhodamine B-doped POFA pumped at 550 nm. Also, wit a GI POF doped with europium chelate of hexafluoroacetylacetone in tris form, we observed superfluorescence, evidenced by spectral narrowing and lifetime shortening. The prospect is that the wide choice of organic dyes and rare earth chelates offers optical amplifiers and superfluorescence sources for a variety of communication and sensor applications.
Multiple sclerosis: Capping of surface immunoglobulin G on macrophages engaged in myelin breakdown

Macrophages were examined for immunoglobulin G (IgG) and albumin in actively demyelinating lesions in two patients with multiple sclerosis (MS) using the peroxidase‐antiperoxidase immunocytochemical technique. In both cases, macrophages were present that stained for cytoplasmic or surface IgG or both. In one case, in which the tissue was rapidly fixed in chilled fixative, macrophages located among myelinated nerve fibers at plaque margins, but not elsewhere in the plaque, revealed surface IgG in the form of caps restricted to one or both poles of the cell. These caps were absent in sections stained for albumin. Because capping implies the presence of a multivalent ligand close to the cell surface and because cap formation was observed only in macrophages contacting myelin sheaths, we suggest that antimyelin antibody cytophilic for macrophages may be present in the central nervous system in MS, and that immune ligand‐mediated phagocytosis may play a role in myelin breakdown in the disease. This study provides the first direct evidence that IgG participates locally in myelin breakdown in MS.
Oscillatory Brain Dynamics during Sentence Reading: A Fixation-Related Spectral Perturbation Analysis

The present study investigated oscillatory brain dynamics during self-paced sentence-level processing. Participants read fully correct sentences, sentences containing a semantic violation and “sentences” in which the order of the words was randomized. At the target word level, fixations on semantically unrelated words elicited a lower-beta band (13–18 Hz) desynchronization. At the sentence level, gamma power (31–55 Hz) increased linearly for syntactically correct sentences, but not when the order of the words was randomized. In the 300–900 ms time window after sentence onsets, theta power (4–7 Hz) was greater for syntactically correct sentences as compared to sentences where no syntactic structure was preserved (random words condition). We interpret our results as conforming with a recently formulated predictive-coding framework for oscillatory neural dynamics during sentence-level language comprehension. Additionally, we discuss how our results relate to previous findings with serial visual presentation vs. self-paced reading.
Bacterial DNA translocation holds increased insulin resistance and systemic inflammatory levels in morbid obese patients.

BACKGROUND Morbidly obese patients show several common comorbidities associated with immunological alterations such as a sustained low-level proinflammatory profile. Bacterial product translocation is frequent in inflammation-related diseases and may aggravate patients' clinical outcome. DESIGN Consecutively admitted morbidly obese patients who presented indications for bariatric surgery were studied. Before surgery, patients were subjected to a modified fasting diet. Patients underwent surgery by sleeve gastrectomy or laparoscopic Roux-en-Y gastric bypass. Clinical and analytical parameters were recorded. Blood samples were collected at baseline, at the end of a 3-month modified fasting period, and 3, 6, and 12 months after surgery. Serum cytokine and endotoxin levels were evaluated by flow cytometry and ELISA, respectively. Bacterial DNA was identified in blood by broad-range PCR of prokaryote 16SrRNA gene and partial sequencing analysis. RESULTS Fifty-eight patients were included in the study. All patients showed a significantly reduced weight and body mass index at each time-point. Postoperative mortality was null. Bacterial DNA translocation rate was 32.8% (19 of 58) at baseline; 13.8% (8 of 58) after the modified fasting period; and 13.8% (8 of 58), 1.8% (1 of 58), and 5.2% (3 of 58) at 3, 6, and 12 months after surgery. Proinflammatory cytokines, serum endotoxin levels, and insulin resistance remained increased in patients with bacterial DNA despite weight loss and were individually affected by the appearance/clearance of bacterial DNA in blood. Multivariate analyses revealed bacterial DNA as an independent significant factor, explaining the systemic cytokine response and the insulin resistance levels in the studied population. CONCLUSION Bacterial DNA translocation holds increased insulin resistance and systemic inflammatory levels in morbidly obese patients despite significant weight loss.
Computation in communication: Spike event coding for programmable analog arrays

This paper presents the computation properties of an asynchronous spike event coding scheme employed for communicating signals between analog blocks in a programmable array. The computation is intrinsic to the spike event communication scheme and is performed without additional hardware. The ability of the communication scheme to perform computation will enhance the computation power of the programmable analog array. Test results from a chip implemented using 0.35/xm CMOS technology are presented.
“So, which one is it?” The effect of alternative incremental architectures in a high-performance game-playing agent

This paper introduces Eve, a highperformance agent that plays a fast-paced image matching game in a spoken dialogue with a human partner. The agent can be optimized and operated in three different modes of incremental speech processing that optionally include incremental speech recognition, language understanding, and dialogue policies. We present our framework for training and evaluating the agent’s dialogue policies. In a user study involving 125 human participants, we evaluate three incremental architectures against each other and also compare their performance to human-human gameplay. Our study reveals that the most fully incremental agent achieves game scores that are comparable to those achieved in human-human gameplay, are higher than those achieved by partially and nonincremental versions, and are accompanied by improved user perceptions of efficiency, understanding of speech, and naturalness of interaction.
Available Data Packet Size Policy for Unsolicited Grant Service in the Power Saving Multi-Channel MAC Protocol

With Multi-channel MAC protocols, transmission pairs can send data packet simultaneously. Hence, higher network throughput can be achieved. The developing of 802.11s standard provides the power saving model multi-channel MAC protocol (PSM-MMAC) framework, which divides into negotiation phase and data phase. All the users select appropriate channels to transmit data in dedicated channel during negotiation phase, then the users will switch the transceivers to the selected channel to transfer data packet by RTS/CTS handshake. While taking the size of data window constraints, therefore how to design the data packet size is the key issue of PSM-MMAC in saturation network case. In this paper, we propose a new policy that can adjust the size of data packet based on the channel occupancy and the fairness of user access for unsolicited Grand Service, which has strict requirements on the delay jitter and maximum reserved traffic rate. We also develop the probabilistic statistical analysis model to compare the performance of previous policy and our proposed policy. Simulation results verify our analysis model, and show our policy has the superior performance of the PSM-MMAC to the previous scheme.
A defeasible reasoning approach for description logic ontologies

Classical reasoning for logic-based KR (Knowledge Representation) systems is in general, monotonic. That is, there is an assumption in these systems that there is complete information about a domain. This means that they generally cannot deal with any new information arising which contradicts with the current information. This is not an appropriate model for reasoning in many applications. Therefore, alternative non-monotonic systems have been investigated which can reason under uncertainty or with incomplete information. Defeasible reasoning is one particular model for implementing non-monotonic reasoning. It is concerned with representing and reasoning with defeasible (non-strict) facts about a domain. The defeasible counterpart of the strict fact: "All birds fly" is the defeasible fact: "Most birds fly" (or the alternative phrasing "Birds usually fly"). We discuss two approaches for defeasible reasoning in the family of logic-based KR languages known as Description Logics (DLs). They are applicable to particular extensions of DLs that allow for the statement of defeasible sentences similar to the aforementioned examples. The approaches are known as prototypical reasoning and presumptive reasoning and are both rooted in the notion of Rational Closure developed by Lehmann and Magidor for an extension of propositional logic. Here we recast their definitions in a DL context and define algorithms for prototypical and presumptive reasoning for DL knowledge bases (also called DL ontologies) that may contain defeasible sentences. In particular, we present a plug-in for the Protégé ontology editor which implements these algorithms for OWL ontologies - the Web Ontology Language (OWL) is a formal standard of languages whose semantic basis is identical to that of DLs. Our plug-in, RaMP, allows the modeller to indicate defeasible information in OWL ontologies and perform logical inferencing to determine what defeasible conclusions one can draw from these ontologies.
New insights into the genetic basis of infertility

Infertility is a disease of the reproductive system characterized by inability to achieve pregnancy after 12 or more months of regular unprotected sexual intercourse. A variety of factors, including ovulation defects, spermatogenic failure, parental age, obesity, and infections have been linked with infertility, in addition to specific karyotypes and genotypes. The study of genes associated with infertility in rodent models has expanded the field of translational genetics in identifying the underlying cause of human infertility problems. Many intriguing aspects of the molecular basis of infertility in humans remain poorly understood; however, application of genetic knowledge in this field looks promising. The growing literature on the genetics of human infertility disorders deserves attention and a critical concise summary is required. This paper provides information obtained from a systematic analysis of the literature related to current research into the genetics of infertility affecting both sexes.
Implicit Racial Attitudes Influence Perceived Emotional Intensity on Other-Race Faces

An ability to accurately perceive and evaluate out-group members' emotions plays a critical role in intergroup interactions. Here we showed that Chinese participants' implicit attitudes toward White people bias their perception and judgment of emotional intensity of White people's facial expressions such as anger, fear and sadness. We found that Chinese participants held pro-Chinese/anti-White implicit biases that were assessed in an evaluative implicit association test (IAT). Moreover, their implicit biases positively predicted the perceived intensity of White people's angry, fearful and sad facial expressions but not for happy expressions. This study demonstrates that implicit racial attitudes can influence perception and judgment of a range of emotional expressions. Implications for intergroup interactions were discussed.
Combined system for optical cutting and multiple-beam optical trapping

In this article we describe a system which enables creation of several optical traps by splitting the laser beam in two parts and by using an acoustooptical deflector in one of these parts. This system is combined with a UV pulse laser so that a complex apparatus for optical trapping and cutting is obtained. Movable lenses ensure independent 3D positioning of a beam focus of the trapping and cutting beam without power losses at the back objective aperture. We present several applications of this system.
Examination of Nasolacrimal Duct Morphometry Using Cone Beam Computed Tomography in Patients With Unilateral Cleft Lip/Palate

Objective: The cleft lip/palate (CLP) deformity negatively affects the anatomy of the nasal cavity and maxilla. The effects of this deformity on the lacrimal system have been unidentified yet. This study aimed to evaluate the morphometric changes in the nasolacrimal duct using cone-beam computed tomography (CBCT) in patients with unilateral CLP. Materials and Methods: Retrospective bilateral measurements of the narrowest transversal diameters and the lengths of the nasolacrimal ducts were made for the affected and unaffected sides of 28 patients with CLP and 28 control patients, using the CBCT images. The measurements were statistically compared. Results: The mean narrowest transversal diameter of the nasolacrimal duct for the affected side of the patients with unilateral CLP was statistically significantly narrower than the unaffected side (P = 0.01). There were no statistically significant differences between the control group and the affected and unaffected sides of patient group with unilateral CLP regarding the nasolacrimal duct diameter. The differences were not statistically significant among all groups regarding the mean nasolacrimal duct length. Conclusion: The diameter of the nasolacrimal duct at the affected side of unilateral CLP was narrower than the unaffected side. According to this result, the CLP deformity can have an effect on the nasolacrimal duct diameter. However, CLP might not affect the nasolacrimal duct length.
Potential for the cultivation of exotic mushroom species by exploitation of Mediterranean agricultural wastes.

Four agricultural wastes abundant in eastern Mediterranean countries, i.e. wheat straw, cotton gin-trash, peanut shells and poplar sawdust, were comparatively evaluated as substrates for the cultivation of selected strains of Pleurotus ostreatus, P. eryngii, P. pulmonarius, Agrocybe aegerita, Lentinula edodes and Volvariella volvacea. Both quantitative and qualitative parameters were examined, i.e. substrate incubation efficacy, earliness, yield, biological efficiency, basidiomata number, weight and size, etc. Wheat straw and cotton gin-trash are the most suitable substrates among those tested for Pleurotus spp. and A. aegerita (the former being more advantageous for high BE's and size of basidiomata, the latter for earliness and length of cultivation cycle), followed by poplar sawdust and peanut shells. Cotton gin-trash proved to be unsuitable for L. edodes which performed far better on wheat straw and poplar sawdust for all parameters examined, whereas V. volvacea on cotton gin-trush and wheat straw. The results, verified for P. ostreatus and P. pulmonarius strains in successive cultivation studies of five Pleurotus strains on cotton gin trash, are encouraging for mushroom production diversification by the exploitation of cotton gin-trash, which is cheap and abundant in the Mediterranean area, as alternative substrate for the cultivation of exotic mushroom species.