Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Response TRAITS and Plant Community Strategy Indicate the Stage of Secondary Succession

Abstract Changes of species composition, plant community strategy and functional response trait turnover were studied in a succession from dry pastures to a forest community (oak-hornbeam forests). The following question was asked: are functional response traits and plant community strategies indicators of TAA (time since agricultural land use abandonment), thus of a specific succession stage. Indirect gradient analysis (DCA) was used in order to observe the position of the relevés along the axis and to correlate it with TAA. It was found that the position of relevés on DCA axis 1 is our proxy for TAA. Correlations (Spearman’s rho) between the occurrence of plant functional traits and TAA were performed. Low-growing herb species with scleromorphic leaves and green or red flowers are the predominant plant type on grassland areas, while plant species with digitate, hydro or mesomorphic leaves and white flowers typically prevail in forest. The proportion of chamaephytes increases immediately after land abandonment (afforestation). In a closed forest stand, there are many more herb species with vegetative propagation (bulbils). Herbal species in those stands most often reward pollinators with pollen. The ecological strategy of the entire plant community changes with spontaneous afforestation. On grassland, stress-tolerant species are dominant. After 10 years, the community is defined as CS and after 200 years as a community with a C-CS strategy. Izvleček Raziskava se ukvarja s spreminjanjem funkcionalnih rastlinskih znakov, ekoloških značilnosti vrst in ekološke strategije združbe skozi posamezne stadije zaraščanja pašnikov v odvisnosti od časa opustitve kmetijske rabe (TAA). V raziskavi smo uporabili multivariatno DCA analizo in opazovali položaj florističnih popisov v DCA prostoru in jih korelirali s TAA. Izračunali smo Spearmanov korelacijski koeficient med pojavnostjo posameznega rastlinskega funkcionalnega znaka in TAA. Nizkorastoče zeliščne vrste s sklerofilnimi listi in cvetovi rumenih in rdečih barv so prevladujoč tip rastlin na pašnikih. V gozdovih prevladujejo vrste z deljenimi, hidro ali mezomorfnimi listi in s svetlejšimi (belimi) cvetovi. Delež hamefitov se v združbi po opustitvi kmetijske rabe močno poveča (proces zaraščanja). V sklenjenem gozdnem sestoju je opazen večji delež zeliščnih vrst, ki se razmnožujejo vegetativno (zarodni brstiči ipd.). Omenjene zeliščne vrste privabljajo opraševalce največkrat s cvetnim prahom. Ekološka strategija celotne združbe se preko sekundarne sukcesije spreminja. Na pašnikih prevladujejo stres-toleratorji. Po desetih letih ima združba strategijo kompetitor/ stres tolerator, po dvesto letih pa kompetitor- kompetitor/ stres tolerator.
CMP-PIM: An Energy-Efficient Comparator-based Processing-In-Memory Neural Network Accelerator

In this paper, an energy-efficient and high-speed comparator-based processing-in-memory accelerator (CMP-PIM) is proposed to efficiently execute a novel hardware-oriented comparator-based deep neural network called CMPNET. Inspired by local binary pattern feature extraction method combined with depthwise separable convolution, we first modify the existing Convolutional Neural Network (CNN) algorithm by replacing the computationally-intensive multiplications in convolution layers with more efficient and less complex comparison and addition. Then, we propose a CMP-PIM that employs parallel computational memory sub-array as a fundamental processing unit based on SOT-MRAM. We compare CMP-PIM accelerator performance on different data-sets with recent CNN accelerator designs. With the close inference accuracy on SVHN data-set, CMP-PIM can get ~ 94× and 3× better energy efficiency compared to CNN and Local Binary CNN (LBCNN), respectively. Besides, it achieves 4.3× speed-up compared to CNN-baseline with identical network configuration.
The protective capacity of high payload FMDV A22 IRQ vaccine in sheep against direct-contact challenge with a heterologous, contemporary FMDV A strain from South East Asia

Foot-and-mouth disease (FMD) is an acute, highly contagious viral disease of domestic and wild cloven-hoofed animals, caused by FMD virus (FMDV). An FMD outbreak can cause major production losses and have significant implications for trade. Vaccination can assist in controlling the disease, and emergency vaccination using high antigen payload vaccines (>6 PD50/dose) is considered an important control approach in the event of an outbreak. In recent years there has been a divergence of serotype A viruses in South East Asia (SEA) into several distinct genetic and antigenic clusters. Numerous variants were found to poorly match serotype A vaccines commonly included in international antigen banks. This study examined the ability of single vaccination with high-potency monovalent A22 IRQ vaccine to protect sheep following challenge with the A/VIT/15/2012 strain, just four days following vaccination. The vaccine proved effective at limiting clinical disease but did not prevent infection.
Pulmonary arteriovenous malformations in children with hereditary hemorrhagic telangiectasia: a longitudinal study

Pulmonary arteriovenous malformations (PAVMs) often occur in children with hereditary hemorrhagic telangiectasia (HHT). A 14-year longitudinal study of PAVMs in children with HHT was undertaken to assess the prevalence, the clinical impact, and progression of these malformations. This was a retrospective, single-center study from May 2002 to December 2016 of 129 children with HHT diagnosed using Curacao criteria and/or confirmed by genetic testing. Transthoracic contrast echocardiography (TTCE) was the primary screening modality in all patients and PAVMs were diagnosed based on Barzilai criteria. Moderately positive TTCE (Barzilai criteria ≥ 2) was confirmed with subsequent contrast chest CT. New PAVMs were diagnosed with a positive TTCE after an initial negative TTCE. Embolization of PAVMs were performed according to HHT consensus guidelines. Of 129 children with HHT, 76 (59%) were found to have PAVMs. Sixty-seven (88%) were positive for PAVMs on initial screening. Of 63 children without PAVMs on initial screening, 31 were followed for >1 year. Nine of the 31 (29%) developed new PAVMs after initial negative study. Thirty-eight (50%) of the total 76 children with PAVMs had or developed lesions large enough to be treated with embolization. Nine patients with PAVMs initially too small to be treated with embolization, developed progression of disease and ultimately were treated with embolization over time. The majority, 60% (23/38), of the children with large PAVMs had no related clinical symptoms. After embolization, 21% (8/38), of patients underwent repeat interventions. Genetic diagnosis, age, and gender were not associated with risk of having PAVM nor with need for repeat interventions. Nearly 60% of children with HHT develop PAVMs. The risk for new PAVMs to develop, small PAVMs to become large, and previously embolized PAVMs to require further intervention remains throughout childhood. Thus, children with HHT require continued follow-up until adulthood.
Transcriptional upregulation of Bag3, a chaperone-assisted selective autophagy factor, in animal models of KY-deficient hereditary myopathy

ABSTRACT The importance of kyphoscoliosis peptidase (KY) in skeletal muscle physiology has recently been emphasised by the identification of novel human myopathies associated with KY deficiency. Neither the pathogenic mechanism of KY deficiency nor a specific role for KY in muscle function have been established. However, aberrant localisation of filamin C (FLNC) in muscle fibres has been shown in humans and mice with loss-of-function mutations in the KY gene. FLNC turnover has been proposed to be controlled by chaperone-assisted selective autophagy (CASA), a client-specific and tension-induced pathway that is required for muscle maintenance. Here, we have generated new C2C12 myoblast and zebrafish models of KY deficiency by CRISPR/Cas9 mutagenesis. To obtain insights into the pathogenic mechanism caused by KY deficiency, expression of the co-chaperone BAG3 and other CASA factors was analyzed in the cellular, zebrafish and ky/ky mouse models. Ky-deficient C2C12-derived clones show trends of higher transcription of CASA factors in differentiated myotubes. The ky-deficient zebrafish model (kyyo1/kyyo1) lacks overt signs of pathology, but shows significantly increased bag3 and flnca/b expression in embryos and adult muscle. Additionally, kyyo1/kyyo1 embryos challenged by swimming in viscous media show an inability to further increase expression of these factors in contrast with wild-type controls. The ky/ky mouse shows elevated expression of Bag3 in the non-pathological exterior digitorum longus (EDL) and evidence of impaired BAG3 turnover in the pathological soleus. Thus, upregulation of CASA factors appears to be an early and primary molecular hallmark of KY deficiency. Summary: Increased transcriptional activation of the tension-mediated autophagy factor Bag3 is shown to be a consistent molecular hallmark of KY deficiency in animal models.
Respiratory Diagnostic Tools in Neuromuscular Disease

Children with neuromuscular disease (NMD) are at risk of acquiring respiratory complications. Both clinical assessments and respiratory diagnostic tests are important to optimize the respiratory health and care of such children. The following respiratory diagnostic tools and their utility for evaluating children with NMD are discussed in this article: lung function testing (spirometry and lung volumes), peak cough flow (PCF), respiratory muscle strength testing, oximetry, capnography, and polysomnography.
Altering gain of the infralimbic-to-accumbens shell circuit alters economically dissociable decision-making algorithms

Significance Synaptic remodeling in the infralimbic-to-accumbens shell (IL–NAcSh) circuit is linked to addiction relapse susceptibility; however, how these changes interact with decision-making computations remains unclear. We develop a neurophysiological assay to measure the strength of a specific circuit at the ensemble level. We then use that assay in combination with a neuroeconomic task to provide causal evidence that synaptic strength of the IL–NAcSh mediates distinct aspects of decision-making information processing. We find that individual differences in IL–NAcSh strength mediate reevaluations behaviorally resolvable from parallel, co-occurring deliberative valuations. An important implication of our work is that acutely delivered circuit-specific plasticity manipulations can produce long-lasting computation-specific effects on certain kinds of choices and can potentially serve as a therapeutic neuromodulation intervention. The nucleus accumbens shell (NAcSh) is involved in reward valuation. Excitatory projections from infralimbic cortex (IL) to NAcSh undergo synaptic remodeling in rodent models of addiction and enable the extinction of disadvantageous behaviors. However, how the strength of synaptic transmission of the IL–NAcSh circuit affects decision-making information processing and reward valuation remains unknown, particularly because these processes can conflict within a given trial and particularly given recent data suggesting that decisions arise from separable information-processing algorithms. The approach of many neuromodulation studies is to disrupt information flow during on-going behaviors; however, this limits the interpretation of endogenous encoding of computational processes. Furthermore, many studies are limited by the use of simple behavioral tests of value which are unable to dissociate neurally distinct decision-making algorithms. We optogenetically altered the strength of synaptic transmission between glutamatergic IL–NAcSh projections in mice trained on a neuroeconomic task capable of separating multiple valuation processes. We found that induction of long-term depression in these synapses produced lasting changes in foraging processes without disrupting deliberative processes. Mice displayed inflated reevaluations to stay when deciding whether to abandon continued reward-seeking investments but displayed no changes during initial commitment decisions. We also developed an ensemble-level measure of circuit-specific plasticity that revealed individual differences in foraging valuation tendencies. Our results demonstrate that alterations in projection-specific synaptic strength between the IL and the NAcSh are capable of augmenting self-control economic valuations within a particular decision-making modality and suggest that the valuation mechanisms for these multiple decision-making modalities arise from different circuits.
Functionalized Tyrosinase-Lignin Nanoparticles as Sustainable Catalysts for the Oxidation of Phenols

Sustainable catalysts for the oxidation of phenol derivatives under environmentally friendly conditions were prepared by the functionalization of lignin nanoparticles with tyrosinase. Lignin, the most abundant polyphenol in nature, is the main byproduct in the pulp and paper manufacturing industry and biorefinery. Tyrosinase has been immobilized by direct adsorption, encapsulation, and layer-by-layer deposition, with or without glutaraldehyde reticulation. Lignin nanoparticles were found to be stable to the tyrosinase activity. After the enzyme immobilization, they showed a moderate to high catalytic effect in the synthesis of catechol derivatives, with the efficacy of the catalyst being dependent on the specific immobilization procedures.
Inhibition of Rumen Methanogenesis and Ruminant Productivity: A Meta-Analysis

Methane (CH4) formed in the rumen and released to the atmosphere constitutes an energy inefficiency to ruminant production. Redirecting energy in CH4 to fermentation products with a nutritional value to the host animal could increase ruminant productivity and stimulate the adoption of CH4-suppressing strategies. The hypothesis of this research was that inhibiting CH4 formation in the rumen is associated with greater ruminant productivity. The primary objective of this meta-analysis was to evaluate how inhibiting rumen methanogenesis relates with the efficiencies of milk production and growth and fattening. A systematic review of peer-reviewed studies in which rumen methanogenesis was inhibited with chemical compounds was conducted. Experiments were clustered based on research center, year of publication, experimental design, feeding regime, type of animal, production response, inhibitor of CH4 production, and method of CH4 measurement. Response variables were regressed against the random experiment effect nested in its cluster, the random effect of the cluster, the linear and quadratic effects of CH4 production, and the random interaction between CH4 production and the experiment nested in the cluster. When applicable, responses were adjusted by intake of different nutrients included as regressors. Inhibiting rumen methanogenesis tended to associate positively with milk production efficiency, although the relationship was influenced by individual experiments. Likewise, a positive relationship between methanogenesis inhibition and growth and fattening efficiency depended on the inclusion and weighting of individual experiments. Inhibiting rumen methanogenesis negatively associated with dry matter intake. Interpretation of the effects of inhibiting methanogenesis on productivity is limited by the availability of experiments simultaneously reporting energy losses in feces, H2, urine and heat production, as well as net energy partition. It is concluded that inhibiting rumen methanogenesis has not consistently translated into greater animal productivity, and more animal performance experiments are necessary to better characterize the relationships between animal productivity and methanogenesis inhibition in the rumen. A more complete understanding of changes in the flows of nutrients caused by inhibiting rumen methanogenesis and their effect on intake also seems necessary to effectively re-channel energy gained from CH4 suppression toward consistent gains in productivity.
Dynamic Resource Sharing in 5G with LSA: Criteria-Based Management Framework

Owing to a steadily increasing demand for efficient spectrum utilization as part of the fifth-generation (5G) cellular concept, it becomes crucial to revise the existing radio spectrum management techniques and provide more flexible solutions for the corresponding challenges. A new wave of spectrum policy reforms can thus be envisaged by producing a paradigm shift from static to dynamic orchestration of shared resources. The emerging Licensed Shared Access (LSA) regulatory framework enables flexible spectrum sharing between a limited number of users that access the same frequency bands, while guaranteeing better interference mitigation. In this work, an advanced user satisfaction-aware spectrum management strategy for dynamic LSA management in 5G networks is proposed to balance both the connected user satisfaction and the Mobile Network Operator (MNO) resource utilization. The approach is based on the MNO decision policy that combines both pricing and rejection rules in the implemented processes. Our study offers a classification built over several types of users, different corresponding attributes, and a number of MNO’s decision scenarios. Our investigations are built on Criteria-Based Resource Management (CBRM) framework, which has been specifically designed to facilitate dynamic LSA management in 5G mobile networks. To verify the proposed model, the results (spectrum utilization, estimated Secondary User price for the future connection, and user selection methodology in case of user rejection process) are validated numerically as we yield important conclusions on the applicability of our approach, which may offer valuable guidelines for efficient radio spectrum management in highly dynamic and heterogeneous 5G environments.
In Vitro Activity of Ceftolozane-Tazobactam against Enterobacter cloacae Complex Clinical Isolates with Different β-Lactam Resistance Phenotypes

The study evaluated the in vitro activity of ceftolozane-tazobactam (C/T) against 94 unique clinical isolates of Enterobacter cloacae complex (ECC). No difference was observed according to the ECC cluster. ABSTRACT The study evaluated the in vitro activity of ceftolozane-tazobactam (C/T) against 94 unique clinical isolates of Enterobacter cloacae complex (ECC). No difference was observed according to the ECC cluster. The in vitro activity greatly varied depending on the β-lactamase-producing profile: 100%, 67%, and 19% of wild-type, extended-spectrum β-lactamase (ESBL)-producing, and AmpC-overproducing strains, respectively, were susceptible to C/T. The use of C/T could be of interest for the treatment of some infections caused by ESBL-producing AmpC-nonoverexpressing ECC isolates.
Evaluation of Ocular Surface Disease in Patients With Glaucoma: Clinical Parameters, Self-report Assessment, and Keratograph Analysis

Purpose: To assess ocular surface disease (OSD) in glaucoma using clinical parameters, self-report assessment, and keratograph analysis. Methods: A total of 30 glaucoma patients and 27 subjects with cataracts (control group) were enrolled in the study. Only glaucoma patients who were using at least 1 topical intraocular pressure–lowering medication were included. An ophthalmological examination was performed, including tear break-up time (BUT), assessment of conjunctival hyperemia and keratitis, and completion of the Ocular Surface Disease Index (OSDI) questionnaire. All the patients underwent keratograph analysis including noninvasive BUT, meibography, tear meniscus height, and redness scale. Quality of life was also assessed in all the patients using National Eye Institute Visual Function Questionnaire (NEI VFQ)-25. The comparison of OSD between the 2 groups was assessed. Results: There was a significant difference in OSD: keratitis and conjunctival hyperemia were worse in the glaucoma group (P=0.009 and 0.008, respectively). The glaucoma group had significantly worse scores on the OSDI questionnaire (32.53±20.75 vs. 20.42±18.77; P=0.007). For the keratograph assessment, the glaucoma group had significantly smaller tear meniscus height (0.22±0.08 vs. 0.24±0.04, respectively; P=0.041); worse bulbar redness (2.06±0.67 vs. 1.70±0.45, respectively; P=0.021); higher meibography grades (2.34±1.01 vs. 1.52±0.64, respectively; P=0.001); and worse noninvasive keratograph tear BUT (5.45±4.16 vs. 8.40±5.65, respectively; P=0.023). Patients with glaucoma had a worse quality of life (60.73±18.25 vs. 76.62±8.03, respectively; P=0.039). Conclusions: Our findings not only confirm the high prevalence of clinical findings of OSD in glaucoma patients but also reveal new objective parameters measured by keratograph analysis.
Genomic organization underlying deletional robustness in bacterial metabolic systems

Significance From the organismal and the anatomical levels down to the molecular level, all complex biological systems manifest astonishing organization and order that are counterintuitive and challenging to explain by evolutionary mechanisms. In this study, we focus specifically on one aspect of this biological organization: the arrangement of metabolic genes in bacterial genomes. We show that this organization ensures a substantially higher robustness to large-scale gene deletions than expected from random genomic ordering. We systematically investigate the possible evolutionary mechanisms behind the emergence of such robust organizations. Our analysis provides several lines of evidence indicating that bacteria may have gained a robust genome organization through pervasive gene loss events. Large-scale DNA deletions and gene loss are pervasive in bacterial genomes. This observation raises the possibility that evolutionary adaptation has altered bacterial genome organization to increase its robustness to large-scale tandem gene deletions. To find out, we systematically analyzed 55 bacterial genome-scale metabolisms and showed that metabolic gene ordering renders an organism’s viability in multiple nutrient environments significantly more robust against tandem multigene deletions than expected by chance. This excess robustness is caused by multiple factors, which include the clustering of essential metabolic genes, a greater-than-expected distance of synthetically lethal metabolic gene pairs, and the clustering of nonessential metabolic genes. By computationally creating minimal genomes, we show that a nonadaptive origin of such clustering could in principle arise as a passive byproduct of bacterial genome growth. However, because genome randomization forces such as translocation and inversion would eventually erode such clustering, adaptive processes are necessary to sustain it. We provide evidence suggesting that this organization might result from adaptation to ongoing gene deletions, and from selective advantages associated with coregulating functionally related genes. Horizontal gene transfer in the presence of gene deletions contributes to sustaining the clustering of essential genes. In sum, our observations suggest that the genome organization of bacteria is driven by adaptive processes that provide phenotypic robustness in response to large-scale gene deletions. This robustness may be especially important for bacterial populations that take advantage of gene loss to adapt to new environments.