Miracle-dz/UniFAR-FTUs huggingface dataset:
When does form reflect function? Acknowledging and supporting ecomorphological assumptions.

Ecomorphology is the study of relationships between organismal morphology and ecology. As such, it is the only way to determine if morphometric data can be used as an informative proxy for ecological variables of interest. To achieve this goal, ecomorphology often depends on, or directly tests, assumptions about the nature of the relationships among morphology, performance and ecology. We discuss three approaches to the study of ecomorphology: morphometry-driven, function-driven, and ecology-driven and study design choices inherent to each approach. We also identify ten assumptions that underlie ecomorphological research: four of these are central to all ecomorphological studies; the remaining six are variably applicable to some of the specific approaches described above. We discuss how these assumptions may impact ecomorphological studies and affect the interpretation of their findings. We also point out some limitations of ecomorphological studies, and highlight some ways by which we can strengthen, validate, or eliminate systematic assumptions.
Comparison of Radiated Electromagnetic Interference (EMI) Generated by Power Converters with Silicon MOSFETs and GaN HEMTs

The increasing switching frequency of power converters always leads to severer radiated electromagnetic interference (EMI), especially with the boom of wide bandgap (WBG) devices. Therefore, the development of radiation model and the analysis of the influence of WBG devices on the radiated EMI is important. This paper proposed a technique of developing the radiation model and compared the radiated EMI generated by converters with silicon MOSFETs and GaN HEMTs. Experiments are carried out to verify the analysis.
Effect of Different Sources Support on Adaptation in Families of Patient With Moderate-to-Severe Dementia in China

Purpose: To examine the support from different sources of Chinese families of patients with moderate-to-severe dementia that most heavily influences the family adaptation and the influence pathway. Method: Two hundred and three families participated in this study. Chinese versions of instruments were used. Structural equation modeling was applied to confirm the effect pathway. Results: More family support, kin support, community support, and social support (narrow sense) were related to greater levels of family adaptation. Family support was the most heavy influence factor (total effect = 0.374), followed by kin support (0.334), social support (0.137), and community support (0.121). Family support and kin support were direct influence factors, while the other 2 were not. Conclusion: All support will promote family adaptation, especially family support and kin support. Interventions improving support from different sources, especially family support and kin support, will promote adaptation in Chinese families of patients with moderate-to-severe dementia.
Spam Email Detection using ID3 Algorithm and Hidden Markov Model

Emails are the way to communicate over the Internet but this method of communication is bothersome by the Spam emails. Spam emails are the waste of memory, money, time and communication bandwidth. Thus, Spam emails needed to be identified and culminated. Hence, use of the ID3 algorithm for making the decision trees and the Hidden Markov Model for calculating the probabilities of the events that may occur is used in this paper as a combination to identify the emails as Spam or ham. The model labels the emails as Spam or ham by calculating total probability of an email using all posteriorly classified words in emails and then supervising all processed emails by making their decision trees. For this purpose, an Enron dataset of 5172 emails is used that contains 2086 Spam and 2086 ham pre-classified emails. The experimental result on the given dataset shows that an accuracy of 89% is obtained on the Spam emails.
Fusion with an albumin‐binding domain improves pharmacokinetics of an αvβ3‐integrin binding fibronectin scaffold protein

Fusion with an albumin‐binding domain (ABD) of streptococcal protein G represents a popular approach for half‐life extension of small protein therapeutics in the organism. To increase the circulation time of engineered αvβ3‐integrin‐binding protein (JCL) based on the 10th human fibronectin type III domain (10Fn3), we have constructed several fusions with ABD with different orientations of the partner proteins and linker length. The recombinant proteins were expressed in Escherichia coli cells and purified by nickel‐affinity chromatography. All fusion proteins bound human serum albumin (HSA) in ELISA assay; however, fusions with longer linkers demonstrated better performance. Interaction of ABD‐L15‐JCL and JCL‐L14‐ABD with HSA was confirmed by analytical size exclusion chromatography and pull‐down assays. Surprisingly, the thermal stability of ABD‐L15‐JCL was dramatically decreased in comparison with JCL and JCL‐L14‐ABD proteins. Pharmacokinetic studies revealed that JCL‐L14‐ABD circulated in murine blood about 10 times longer than ABD‐L15‐JCL and 960 times longer than JCL. Biodistribution studies of JCL‐L14‐ABD in mice revealed its increased level in blood and a decreased accumulation in liver and kidneys in comparison with JCL. Obtained results demonstrate the utility of the fusion with ABD for half‐life extension of the binding proteins based on 10Fn3.
Bortezomib attenuates renal interstitial fibrosis in kidney transplantation via regulating the EMT induced by TNF‐α‐Smurf1‐Akt‐mTOR‐P70S6K pathway

Allograft interstitial fibrosis was characterized by massive extracellular matrix deposition caused by activated fibroblasts and myofibroblasts. Epithelial‐mesenchymal transition (EMT) is recognized as an important source of myofibroblasts contributing to the pathogenesis of allograft interstitial fibrosis. Smad ubiquitination regulatory factor 1 (Smurf1) has been recently reported to be involved in the progression of EMT. Our study was to detect the effect of Bortezomib and Smurf1 in the EMT and allograft interstitial fibrosis. Biomarkers of EMT, as well as Smurf1, were examined in human proximal tubular epithelial cells (HK‐2) treated with tumour necrosis factor‐alpha (TNF‐α) in various doses or at various time points by Western Blotting or qRT‐PCR. We knockdown or overexpressed Smurf1 in HK‐2 cells. Furthermore, rat renal transplant model was established and intervened by Bortezomib. Allograft tissues from human and rats were also collected and prepared for HE, Masson's trichrome, immunohistochemical staining and western blotting assays. As a result, we found that TNF‐α significantly promoted the development of EMT in a time‐dependent and dose‐dependent manner through Smurf1/Akt/mTOR/P70S6K signalling pathway. More importantly, Bortezomib alleviated the progression of EMT and allograft interstitial fibrosis in vivo and in vitro by inhibiting the production of TNF‐α and expression of Smurf1. In conclusion, Smurf1 plays a critical role in the development of EMT induced by TNF‐α. Bortezomib can attenuate the Sumrf1‐mediated progression of EMT and renal allograft interstitial fibrosis, which could be suggested as a novel choice for the prevention and treatment of renal allograft interstitial fibrosis.
Fatigue in multiple sclerosis: The role of thalamus

Fatigue is very common in multiple sclerosis (MS) and is often considered as its most disabling symptom. Over the last 20 years, an increasing number of studies have evaluated the pathogenetic bases of MS-related fatigue. Converging evidence from neurophysiology and neuroimaging research suggests that a dysfunction in a cortico-subcortical pathway, centered on thalamus, is involved in the pathogenesis of fatigue. However, type and significance of such dysfunction remain unknown, and some studies reported an increase in the activity and connectivity within the thalamic network, whereas others suggested its reduction. Hereby, we review the results of neuroimaging studies supporting the different hypotheses about the role of thalamic network in the pathophysiology of MS-related fatigue and discuss limitations and shortcomings of available data, highlighting the key challenges in the field and the directions for future research.
Identifying a marked inflammation mediated cardiac dysfunction during the development of arthritis in collagen-induced arthritis mice.

OBJECTIVES Systemic inflammation is very closely linked to the increased risk of cardiovascular diseases (CVD) in rheumatoid arthritis (RA). We investigated the cardiac changes during the development of arthritis in collagen-induced arthritis (CIA) mice to explore the potential role of inflammation on cardiac dysfunction in RA. METHODS Arthritis severity was evaluated using clinical indices, micro-computed tomography and histopathology. Cardiac function was determined by transthoracic echocardiography at weeks 5, 7, 9 and 11 after immunisation in mice. At week 7 (day 50), mice joints and hearts were removed for pathological study, and cardiomyocytes and cardiac fibroblasts were isolated using Langendorff perfusion method ex vivo to measure the expression of inflammatory and cardiac-related genes by real time PCR. The expression of key molecule in cardiac dysfunction (β-MHC) was also tested in H9c2 cardiomyocyte treated with sera derived from CIA mice or RA patients. RESULTS At day 50 after immunisation, cardiac function in CIA mice was prominently reduced as evidenced by decreased ejection fraction (EF) and fractional shortening (FS), increased left ventricular end-systolic volume (LVESV) and internal systolic diameter (LVIDs). Accordingly, enhanced inflammatory cell infiltration and fibrosis were identified in ventricular tissues pathologically, and increased inflammatory gene expression including TNF-α, IL-6, IL-17 and MMP3 was detected in isolated ventricular cardiomyocytes and cardiac fibroblasts from CIA mice. Furthermore, H9c2 cells treated with sera from CIA mice or RA patients exhibited high levels of β-MHC. CONCLUSIONS Joint inflammation is associated with an obvious cardiac dysfunction and enhanced inflammation infiltration and inflammatory cytokine production in cardiomyocytes and cardiac fibroblasts during CIA development. Our data provide the direct evidence that inflammation contributes to the development of cardiac diseases in RA patients.
Instruction-Cache Attack on DSA Adopting Square-Multiply Method

DSA is one of the most widely used digital signature scheme. Based on previous work, this paper introduced the principle of Instruction-Cache timing attack and presented some key techniques in Instruction-Cache monitoring and high precision timing. Then an attack on DSA was presented, and an algorithm for recovering nonce was proposed. In the end, an attack experiment was launched. The results demonstrated that the attack is realistic, feasible and effective.
TIMELESS mutation alters phase responsiveness and causes advanced sleep phase

Significance TIMELESS has a clear role in the regulation of circadian rhythms in Drosophila, but its role in mammalian circadian regulation remains unclear. A mutation identified in a small family with advanced sleep phase causes cytoplasmic accumulation of TIMELESS. We confirm that TIMELESS can bind the critical negative regulators of the circadian clock, PER2 and CRY2, and destabilize them when TIMELESS remains in the cytoplasm. The mutant mouse model has a phase advance of sleep–wake behavior and altered sensitivity to light pulses, but normal period length. These data demonstrate that TIMELESS may play a role in regulating minor phase changes and therefore contribute to the maintenance of circadian rhythmicity in mammals. Many components of the circadian molecular clock are conserved from flies to mammals; however, the role of mammalian Timeless remains ambiguous. Here, we report a mutation in the human TIMELESS (hTIM) gene that causes familial advanced sleep phase (FASP). Tim CRISPR mutant mice exhibit FASP with altered photic entrainment but normal circadian period. We demonstrate that the mutation prevents TIM accumulation in the nucleus and has altered affinity for CRY2, leading to destabilization of PER/CRY complex and a shortened period in nonmature mouse embryonic fibroblasts (MEFs). We conclude that TIM, when excluded from the nucleus, can destabilize the negative regulators of the circadian clock, alter light entrainment, and cause FASP.
Comparison of hypoxic effects induced by chemical and physical hypoxia on cardiomyocytes.

The degree and duration of chemical hypoxia induced by sodium dithionite (Na2S2O4) have not been reported. It is not yet clear how much reduction in the O2 concentration (physical hypoxia) can lead to hypoxia in cultured cardiomyocytes. In this study, oxygen microelectrodes were used to measure changes in the O2 concentration in media containing different concentrations of Na2S2O4. Then, hypoxic effects of 0.8, 1.0, 2.0 mM Na2S2O4 or 1%, 3%, and 5% O2 in cultured cardiomyocytes from neonatal rats were observed and compared. The results showed that the O2 concentration failed to remain constant by Na2S2O4 treatment during the 180-minute observation period. Only the 2.0 mM Na2S2O4 group significantly increased the expression of hypoxia-inducible factor 1α (HIF-1α) and hypoxic responses. Notably, 3% O2 only significantly increased the expression of HIF-1α in cardiomyocytes, while 1% O2 not only increased the expression of HIF-1α but also increased the apoptotic rate in cardiomyocytes. These results suggest that Na2S2O4 is not suitable for establishing a hypoxic model in cultured neonatal rat cardiomyocytes, neonatal rat cardiomyocytes cultured at or below 1% O2 induced significant hypoxic effects, which can be used as a starting O2 concentration for establishing a hypoxic cell model.
Outdoor navigation of a mobile robot between buildings based on DGPS and odometry data fusion

The authors aim at map based outdoor navigation of a mobile robot. In navigation, robot position is fundamentally obtained by odometry. However, the position is misaligned as the robot moves because odometry has cumulative error. DGPS measurement data may cancel its position error. The framework of EKF is used for the modification and the fusion between odometry and DGPS measurement data. The DGPS measurement data, however, could have large error because of multipath near buildings. In this paper, the authors propose a method which eliminates erroneous DGPS measurement data when odometry robot position is fused, and confirm the validity of this approach.
Impact of Cocoa Products Intake on Plasma and Urine Metabolites: A Review of Targeted and Non-Targeted Studies in Humans

Cocoa is continuously drawing attention due to growing scientific evidence suggesting its effects on health. Flavanols and methylxanthines are some of the most important bioactive compounds present in cocoa. Other important bioactives, such as phenolic acids and lactones, are derived from microbial metabolism. The identification of the metabolites produced after cocoa intake is a first step to understand the overall effect on human health. In general, after cocoa intake, methylxanthines show high absorption and elimination efficiencies. Catechins are transformed mainly into sulfate and glucuronide conjugates. Metabolism of procyanidins is highly influenced by the polymerization degree, which hinders their absorption. The polymerization degree over three units leads to biotransformation by the colonic microbiota, resulting in valerolactones and phenolic acids, with higher excretion times. Long term intervention studies, as well as untargeted metabolomic approaches, are scarce. Contradictory results have been reported concerning matrix effects and health impact, and there are still scientific gaps that have to be addresed to understand the influence of cocoa intake on health. This review addresses different cocoa clinical studies, summarizes the different methodologies employed as well as the metabolites that have been identified in plasma and urine after cocoa intake.
Casein-Conjugated Gold Nanoparticles for Amperometric Detection of Leishmania infantum

Sensitive and reliable approaches targeting the detection of Leishmania are critical for effective early diagnosis and treatment of leishmaniasis. In this frame, this paper describes a rapid quantification assay to detect Leishmania parasites based on the combination of the electrocatalytic ability of gold nanoparticles (AuNPs) to act as a catalyst for the hydrogen formation reaction along with the specificity of the interaction between casein and the major surface protease of the Leishmania parasite, GP63. First, pure and casein-modified AuNPs were prepared and characterized by scanning electron microscopy and ultraviolet–visible spectroscopy. Then, casein-conjugated AuNPs were incubated with Leishsmania parasites in solution; the formed complex was collected by centrifugation, treated by acidic solution, and the pelleted AuNPs were placed on screen-printed carbon electrodes (SPCEs) and chronoamperometric measurements were carried out. Our results suggest that it is possible to detect Leishmania parasites, with a limit less than 1 parasite/mL. A linear response over a wide concentration interval, ranging from 2 × 10−2 to 2 × 105 parasites/mL, was achieved. Additionally, a pretreatment of Leishmania parasites with Amphotericin B, diminished their interaction with casein. This findings and methodology are very useful for drug efficacy assessment.
In vitro evaluation of the effects of Yucca schidigera and inulin on the fermentation potential of the faecal microbiota of dogs fed diets with low or high protein concentrations

ABSTRACT This in vitro study aimed to evaluate the effects of Yucca schidigera powder (YSP) and inulin (IN) on protein fermentation metabolites (short-chain fatty acids [SCFA] and branched-chain fatty acids, phenolic and indolic compounds, biogenic amines, ammonia and pH) by using faecal inocula from dogs fed either a low (L) or a high (H) protein diet (crude protein 201 or 377 g/kg as fed). Four treatments for each diet were evaluated in an in vitro batch culture system over 24 h: (1) control with no addition of substrates; (2) 4 g YSP/l; (3) 5 g IN/l; (4) 4 g YSP/l in combination with 5 g IN/l of faecal culture of dogs fed Diet L or H. Several changes in fermentation metabolites were analysed. Samples incubated with the faecal inocula of dogs fed Diet L produced higher concentrations of total SCFA, propionate (p = 0.001), acetate (p ≤ 0.001), d-lactate (p = 0.041) and indole (p = 0.003), whereas pH (p = 0.004) was decreased. Supplementation of IN increased the content of putrescine, d- and l-lactate, total SCFA, acetate, propionate, n-butyrate (p ≤ 0.001) and n-valerate (p = 0.003), while i-valerate, indole and pH (p ≤ 0.001) were reduced. Ammonia was lower (p = 0.013) in samples with faecal inocula from dogs fed Diet H and further reduced by the addition of IN (p ≤ 0.001). Samples with faecal inocula from dogs fed Diet L had a fewer quotient of ammonia and total SCFA (p = 0.040). Supplementation of YSP (p = 0.021), IN (p ≤ 0.001) and YSP in combination with IN (p = 0.047) led to a higher reduction of the quotient of ammonia and total SCFA. In conclusion, dietary protein concentration and the supplementation of IN resulted in a stimulation of fermentation while YSP appeared to have only minor effects.
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes

Abstract Summary Distinguishing biologically relevant interfaces from crystallographic ones in biological complexes is fundamental in order to associate cellular functions to the correct macromolecular assemblies. Recently, we described a detailed study reporting the differences in the type of intermolecular residue–residue contacts between biological and crystallographic interfaces. Our findings allowed us to develop a fast predictor of biological interfaces reaching an accuracy of 0.92 and competitive to the current state of the art. Here we present its web-server implementation, PRODIGY-CRYSTAL, aimed at the classification of biological and crystallographic interfaces. PRODIGY-CRYSTAL has the advantage of being fast, accurate and simple. This, together with its user-friendly interface and user support forum, ensures its broad accessibility. Availability and implementation PRODIGY-CRYSTAL is freely available without registration requirements at https://haddock.science. uu.nl/services/PRODIGY-CRYSTAL.
Therapeutic Effects of rAAV-Mediated Concomittant Gene Transfer and Overexpression of TGF-β and IGF-I on the Chondrogenesis of Human Bone-Marrow-Derived Mesenchymal Stem Cells

Application of chondroreparative gene vectors in cartilage defects is a powerful approach to directly stimulate the regenerative activities of bone-marrow-derived mesenchymal stem cells (MSCs) that repopulate such lesions. Here, we investigated the ability of combined recombinant adeno-associated virus (rAAV) vector-mediated delivery of the potent transforming growth factor beta (TGF-β) and insulin-like growth factor I (IGF-I) to enhance the processes of chondrogenic differentiation in human MSCs (hMSCs) relative to individual candidate treatments and to reporter (lacZ) gene condition. The rAAV-hTGF-β and rAAV-hIGF-I vectors were simultaneously provided to hMSC aggregate cultures (TGF-β/IGF-I condition) in chondrogenic medium over time (21 days) versus TGF-β/lacZ, IGF-I/lacZ, and lacZ treatments at equivalent vector doses. The cultures were then processed to monitor transgene (co)-overexpression, the levels of biological activities in the cells (cell proliferation, matrix synthesis), and the development of a chondrogenic versus osteogenic/hypertrophic phenotype. Effective, durable co-overexpression of TGF-β with IGF-I via rAAV enhanced the proliferative, anabolic, and chondrogenic activities in hMSCs versus lacZ treatment and reached levels that were higher than those achieved upon single candidate gene transfer, while osteogenic/hypertrophic differentiation was delayed over the period of time evaluated. These findings demonstrate the potential of manipulating multiple therapeutic rAAV vectors as a tool to directly target bone-marrow-derived MSCs in sites of focal cartilage defects and to locally enhance the endogenous processes of cartilage repair.