Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealing catastrophic failure of leaf networks under stress

Significance Water sustains photosynthesis and growth of land plants, but it must be transported from the soil to leaves under high tension. Drying soil leads to an increase in water tension, exposing plants to the problem of breakage of the water column, causing embolisms that cut off water supply, leading to tissue death during drought. The ability of leaves to resist embolism formation is a key adaptive axis in plant evolution, and yet the process itself has never been visualized in the leaf venation. We describe a new optical method that allows the evolution and spread of embolism in the entire leaf network to be mapped, thus revealing general rules in the sequence of leaf vein transport failure. The intricate patterns of veins that adorn the leaves of land plants are among the most important networks in biology. Water flows in these leaf irrigation networks under tension and is vulnerable to embolism-forming cavitations, which cut off water supply, ultimately causing leaf death. Understanding the ways in which plants structure their vein supply network to protect against embolism-induced failure has enormous ecological and evolutionary implications, but until now there has been no way of observing dynamic failure in natural leaf networks. Here we use a new optical method that allows the initiation and spread of embolism bubbles in the leaf network to be visualized. Examining embolism-induced failure of architecturally diverse leaf networks, we found that conservative rules described the progression of hydraulic failure within veins. The most fundamental rule was that within an individual venation network, susceptibility to embolism always increased proportionally with the size of veins, and initial nucleation always occurred in the largest vein. Beyond this general framework, considerable diversity in the pattern of network failure was found between species, related to differences in vein network topology. The highest-risk network was found in a fern species, where single events caused massive disruption to leaf water supply, whereas safer networks in angiosperm leaves contained veins with composite properties, allowing a staged failure of water supply. These results reveal how the size structure of leaf venation is a critical determinant of the spread of embolism damage to leaves during drought.
Coordinated Linear Precoding in Downlink Multicell MIMO-OFDMA Networks

We consider coordinated linear precoding in downlink multicell multiple-input multiple-output orthogonal frequency-division multiple access (MIMO-OFDMA) systems, where multiple base stations (BSs) coordinate to mitigate the co-channel interference. Two nonconvex rate optimization problems with per-cell power constraints are addressed: weighted sum rate maximization (WSRM) and maximizing the weighted sum of the minimal user rates (MWSMR) of the coordinated cells. We propose two iterative algorithms to achieve suboptimal solutions for the WSRM problem. One attempts to solve the Karush-Kuhn-Tucker (KKT) conditions of the problem and the other is an alternating maximization algorithm based on the idea of the classical Blahut-Arimoto algorithm. The distributed implementations of the two algorithms are also discussed. Moreover, an iterative algorithm based on alternating maximization is proposed to solve the MWSMR problem. Finally, simulation results are presented to demonstrate the effectiveness of the proposed algorithms.
Determining the Optimal Inhibitory Frequency for Cancerous Cells Using Tumor Treating Fields (TTFields)

Tumor Treating Fields (TTFields) are an effective treatment modality delivered via the continuous, noninvasive application of low-intensity (1-3 V/cm), alternating electric fields in the frequency range of several hundred kHz. The study of TTFields in tissue culture is carried out using the TTFields in vitro application system, which allows for the application of electric fields of varying frequencies and intensities to ceramic Petri dishes with a high dielectric constant (Ɛ > 5,000). Cancerous cell lines plated on coverslips at the bottom of the ceramic Petri dishes are subjected to TTFields delivered in two orthogonal directions at various frequencies to facilitate treatment outcome tests, such as cell counts and clonogenic assays. The results presented in this report demonstrate that the optimal frequency of the TTFields with respect to both cell counts and clonogenic assays is 200 kHz for both ovarian and glioma cells.
Growth Kinetics and Transmission Potential of Existing and Emerging Field Strains of Infectious Laryngotracheitis Virus

Attenuated live infectious laryngotracheitis virus (ILTV) vaccines are widely used in the poultry industry to control outbreaks of disease. Natural recombination between commercial ILTV vaccines has resulted in virulent recombinant viruses that cause severe disease, and that have now emerged as the dominant field strains in important poultry producing regions in Australia. Genotype analysis using PCR—restriction fragment length polymorphism has shown one recombinant virus (class 9) has largely replaced the previously dominant class 2 field strain. To examine potential reasons for this displacement we compared the growth kinetics and transmission potential of class 2 and class 9 viruses. The class 9 ILTV grew to higher titres in cell culture and embryonated eggs, but no differences were observed in entry kinetics or egress into the allantoic fluid from the chorioallantoic membrane. In vivo studies showed that birds inoculated with class 9 ILTV had more severe tracheal pathology and greater weight loss than those inoculated with the class 2 virus. Consistent with the predominance of class 9 field strains, birds inoculated with 102 or 103 plaque forming units of class 9 ILTV consistently transmitted virus to in-contact birds, whereas this could only be seen in birds inoculated with 104 PFU of the class 2 virus. Taken together, the improved growth kinetics and transmission potential of the class 9 virus is consistent with improved fitness of the recombinant virus over the previously dominant field strain.
Urinary Exosomal MicroRNA Profiling in Incipient Type 2 Diabetic Kidney Disease

Background Albuminuria is an early sign but not a strong predictor of diabetic kidney disease (DKD). Owing to their high stability, urinary exosomal miRNAs can be useful predictors of the progression of early-stage DKD to renal failure; fluid biopsies are ideal for detecting abnormalities in these miRNAs. The aim of this study was to identify novel differentially expressed miRNAs as urine biomarkers for type 2 DKD by comparing between patients of type 2 diabetes (T2D) with and without macroalbuminuria. Methods Ten patients with T2D, including five who had no renal disease and five with macroalbuminuria (DKD G1-2A3), were selected for this study. Exosome- (UExo-) derived miRNA profiles were used to identify candidate biomarkers, a subset of which was verified using quantitative reverse transcription PCR. Results A total of 496 UExo-derived miRNA species were found to be differentially expressed (>2-fold) in patients with DKD, compared to those with T2D. A validation analysis revealed that three miRNAs (miR-362-3p, miR-877-3p, and miR-150-5p) were upregulated and one (miR-15a-5p) was downregulated. These miRNAs might regulate DKD through p53, mTOR, and AMPK pathways. Conclusions In conclusion, UExo-derived miRNAs were altered in type 2 DKD. MiR-362-3p, miR-877-3p, miR-150-5p, and miR-15a-5p might be novel biomarkers for incipient DKD.
Disentangling the effects of multiple environmental drivers on population changes within communities

The effects of different environmental drivers on the changes in species' population abundances can be difficult to disentangle as they often act simultaneously. Researchers have built statistical models that include environmental variables (such as annual temperature) or species attributes (such as a species' temperature preference), which are assumed to detect the impacts of specific drivers (such as climate change). However, these approaches are often applied separately or, if combined, not explicitly compared. We show the complementary insights gained by applying both these approaches to a community dataset on Danish terrestrial birds. We use our analysis to compare the relative importance of climate change and agricultural land-use change for the abundance changes within the community between 1983 and 2013. Population models were fitted to the community data of species' annual abundances with predictors comprising: species attributes (species' temperature and habitat preferences), environmental variables (climatic and agricultural land-use change variables) or both. Relationships between species' abundances and environmental variables were used to identify the drivers associated with average abundance changes of species in the community. Relationships between species' abundances and their attributes were used to understand the drivers causing interspecific variation in abundance changes. Warmer winters were positively associated with community-level abundances, and warm-adapted species had more positive abundance changes than cold-adapted ones. Agricultural land-use area was negatively associated with community-level abundances, and birds using a high proportion of meadow and habitat specialists had more negative abundance changes than birds using other habitats and habitat generalists. Effect sizes of environmental variables were larger for agricultural land-use change while those of species attributes were larger for climate change. The environmental data approach suggested that agricultural land-use change has decreased the average abundances of species in the community, affecting total community size while the species attribute-based approach suggested that climate change has caused variation in abundance among species, affecting community composition. Environmental variables and species attributes that are hypothesized to link to specific drivers can be used together to provide complementary information on the impacts of different drivers on communities.
An ecoimmunological approach to study evolutionary and ancient links between coagulation, complement and Innate immunity

ABSTRACT Coagulation, complement, and innate immunity are tightly interwoven and form an alliance that can be traced back to early eukaryotic evolution. Here we employed an ecoimmunological approach using Tissue Factor Pathway Inhibitor (TFPI)-1-derived peptides from the different classes of vertebrates (i.e. fish, reptile, bird, and mammals) and tested whether they can boost killing of various human bacterial pathogens in plasma. We found signs of species-specific conservation and diversification during evolution in these peptides that significantly impact their antibacterial activity. Though all peptides tested executed bactericidal activity in mammalian plasma (with the exception of rodents), no killing was observed in plasma from birds, reptiles, and fish, pointing to a crucial role for the classical pathway of the complement system. We also observed an interference of these peptides with the human intrinsic pathway of coagulation though, unlike complement activation, this mechanism appears not to be evolutionary conserved.
Multi-Approaches Analysis Reveals Local Adaptation in the Emmer Wheat (Triticum dicoccoides) at Macro- but not Micro-Geographical Scale

Detecting local adaptation and its spatial scale is one of the most important questions of evolutionary biology. However, recognition of the effect of local selection can be challenging when there is considerable environmental variation across the distance at the whole species range. We analyzed patterns of local adaptation in emmer wheat, Triticum dicoccoides, at two spatial scales, small (inter-population distance less than one km) and large (inter-population distance more than 50 km) using several approaches. Plants originating from four distinct habitats at two geographic scales (cold edge, arid edge and two topographically dissimilar core locations) were reciprocally transplanted and their success over time was measured as 1) lifetime fitness in a year of planting, and 2) population growth four years after planting. In addition, we analyzed molecular (SSR) and quantitative trait variation and calculated the Q ST/F ST ratio. No home advantage was detected at the small spatial scale. At the large spatial scale, home advantage was detected for the core population and the cold edge population in the year of introduction via measuring life-time plant performance. However, superior performance of the arid edge population in its own environment was evident only after several generations via measuring experimental population growth rate through genotyping with SSRs allowing counting the number of plants and seeds per introduced genotype per site. These results highlight the importance of multi-generation surveys of population growth rate in local adaptation testing. Despite predominant self-fertilization of T. dicoccoides and the associated high degree of structuring of genetic variation, the results of the Q ST - F ST comparison were in general agreement with the pattern of local adaptation at the two spatial scales detected by reciprocal transplanting.
Trypanosoma cruzi-Infected Pregnant Women without Vector Exposure Have Higher Parasitemia Levels: Implications for Congenital Transmission Risk

Background Congenital transmission is a major source of new Trypanosoma cruzi infections, and as vector and blood bank control continue to improve, the proportion due to congenital infection will grow. A major unanswered question is why reported transmission rates from T. cruzi-infected mothers vary so widely among study populations. Women with high parasite loads during pregnancy are more likely to transmit to their infants, but the factors that govern maternal parasite load are largely unknown. Better understanding of these factors could enable prioritization of screening programs to target women most at risk of transmission to their infants. Methodology/Principal Findings We screened pregnant women presenting for delivery in a large urban hospital in Bolivia and followed infants of infected women for congenital Chagas disease. Of 596 women screened, 128 (21.5%) had confirmed T. cruzi infection; transmission occurred from 15 (11.7%) infected women to their infants. Parasite loads were significantly higher among women who transmitted compared to those who did not. Congenital transmission occurred from 31.3% (9/29), 15.4% (4/26) and 0% (0/62) of women with high, moderate and low parasite load, respectively (χx2 for trend 18.2; p<0.0001). Twin births were associated with higher transmission risk and higher maternal parasite loads. Infected women without reported vector exposure had significantly higher parasite loads than those who had lived in an infested house (median 26.4 vs 0 parasites/mL; p<0.001) with an inverse relationship between years of living in an infested house and parasite load. Conclusions/Significance We hypothesize that sustained vector-borne parasite exposure and repeated superinfection by T. cruzi may act as an immune booster, allowing women to maintain effective control of the parasite despite the down-regulation of late pregnancy.
Pelvic Inflammatory Disease: Identifying Research Gaps—Proceedings of a Workshop Sponsored by Department of Health and Human Services/National Institutes of Health/National Institute of Allergy and Infectious Diseases, November 3–4, 2011

Abstract In November 2011, the National Institutes of Health convened a workshop of basic researchers, epidemiologists, and clinical experts in pelvic inflammatory disease to identify research gaps hindering advances in diagnosis, treatment, and prevention. This article summarizes the presentations, discussions, and conclusions of this group and highlights significant controversies that reveal aspects of pelvic inflammatory disease research that would most greatly benefit from the application of newer molecular, immunologic, and radiologic techniques. Multiple limitations to performing new clinical trials exist; however, emerging data from ongoing clinical trials will add to the current body of knowledge regarding prevention and treatment strategies. In addition, use of established health care databases could serve as a valuable tool for performance of unbiased epidemiologic outcome studies.
Video Tracking Protocol to Screen Deterrent Chemistries for Honey Bees.

The European honey bee, Apis mellifera L. , is an economically and agriculturally important pollinator that generates billions of dollars annually. Honey bee colony numbers have been declining in the United States and many European countries since 1947. A number of factors play a role in this decline, including the unintentional exposure of honey bees to pesticides. The development of new methods and regulations are warranted to reduce pesticide exposures to these pollinators. One approach is the use of repellent chemistries that deter honey bees from a recently pesticide-treated crop. Here, we describe a protocol to discern the deterrence of honey bees exposed to select repellent chemistries. Honey bee foragers are collected and starved overnight in an incubator 15 h prior to testing. Individual honey bees are placed into Petri dishes that have either a sugar-agarose cube (control treatment) or sugar-agarose-compound cube (repellent treatment) placed into the middle of the dish. The Petri dish serves as the arena that is placed under a camera in a light box to record the honey bee locomotor activities using video tracking software. A total of 8 control and 8 repellent treatments were analyzed for a 10 min period with each treatment was duplicated with new honey bees. Here, we demonstrate that honey bees are deterred from the sugar-agarose cubes with a compound treatment whereas honey bees are attracted to the sugar-agarose cubes without an added compound.
Impact of the Seven-valent Pneumococcal Conjugate Vaccine on Acute Otitis Media in Japanese Children: Emergence of Serotype 15A Multidrug-resistant Streptococcus pneumoniae in Middle Ear Fluid Isolates

Background: Streptococcus pneumoniae is one of the most common bacteria causing acute otitis media (AOM). In Japan, a 7-valent pneumococcal conjugate vaccine (PCV7) was introduced for voluntary vaccination of children in 2010, and it became a recommended vaccination in April 2013. We surveyed the serotypes and antimicrobial susceptibility profile of S. pneumoniae isolates obtained from the middle ear fluid of Japanese children with AOM. Methods: Between April and September 2013, a total of 176 S. pneumoniae isolates were obtained from the middle ear fluid of children aged 0–3 years with AOM. Isolates were collected from various regions of Japan. Minimum inhibitory concentrations were measured by the broth microdilution method. Serotyping was performed by observing the Quellung reaction. Results: Although 45.5% of the strains were susceptible to penicillin G, 42.6% were penicillin-intermediate strains and 11.9% were penicillin-resistant strains. Serotype 19A (27.3%), serotype 15A (14.2%) and serotype 3 (11.9%) showed a high frequency. Although PCV7 types only accounted for 4.5% of all strains, 44.9% were PCV13 types and 55.1% were non-PCV types. Serotype 15A strains were 100% nonsusceptible to penicillin G and all of these strains showed multidrug resistance. Serotype 15A was frequent in children up to 1 year old. Conclusion: After this research was completed, PCV7 was switched to a PCV13 that also contained serotype 3 and serotype 19A. We need to consider the possibility that serotype 15A, which is not included in PCV13, may increase and cause intractable AOM in the future.
Traffic management for TCP/IP over satellite ATM networks

Several Ka-band satellite systems have been proposed that will use ATM technology to seamlessly transport Internet traffic. The ATM UBR, GFR, and ABR service categories have been designed for data. However, several studies have reported poor TCP performance over satellite ATM networks. We describe techniques to improve TCP performance over satellite ATM networks. We first discuss the various design options available for TCP end systems, IP-ATM edge devices, as well as ATM switches for long-latency connections. We discuss buffer management policies, guaranteed rate services, and the virtual source/virtual destination option in ATM. We present a comparison of ATM service categories for TCP transport over satellite links. The main goal of this article is to discuss design and performance issues for the transport of TCP over UBR, GFR, and ABR services for satellite ATM networks.
Galleria mellonella as an infection model to investigate virulence of Vibrio parahaemolyticus

ABSTRACT Non-toxigenic V. parahaemolyticus isolates (tdh −/trh −/T3SS2−) have recently been isolated from patients with gastroenteritis. In this study we report that the larvae of the wax moth (Galleria mellonella) are susceptible to infection by toxigenic or non-toxigenic clinical isolates of V. parahaemolyticus. In comparison larvae inoculated with environmental isolates of V. parahaemolyticus did not succumb to disease. Whole genome sequencing of clinical non-toxigenic isolates revealed the presence of a gene encoding a nudix hydrolase, identified as mutT. A V. parahaemolyticus mutT mutant was unable to kill G. mellonella at 24 h post inoculation, indicating a role of this gene in virulence. Our findings show that G. mellonella is a valuable model for investigating screening of possible virulence genes of V. parahaemolyticus and can provide new insights into mechanisms of virulence of atypical non-toxigenic V. parahaemolyticus. These findings will allow improved genetic tests for the identification of pathogenic V. parahaemolyticus to be developed and will have a significant impact for the scientific community.
The sialoadhesin CD33 is a myeloid‐specific inhibitory receptor

Activating and inhibitory receptors act in concert to regulate cellular activation. Inhibitory receptors are characterized by the presence of a characteristic sequence known as an immunoreceptor tyrosine‐based inhibitory motif (ITIM) in their cytoplasmic tail. Phosphorylated ITIM serve as docking sites for the SH2‐containing phosphatases which then inhibit signal transduction. CD33 is a member of the immunoglobulin superfamily and contains two immunoglobulin‐like domains, a transmembrane region and a cytoplasmic tail that has two potential ITIM sequences. CD33 expression is restricted to cells of myelomonocytic lineage. The precise function of CD33 is unknown although it is a lectin that binds sialic acid residues in N‐ and O‐glycans on cell surfaces. Co‐immunoprecipitation studies demonstrate that CD33 associates with the SH2‐containing tyrosine phosphatase SHP‐1 in monocytes. The proximal ITIM is necessary and sufficient for SHP‐1 binding which is mediated by the aminoterminal SH2 domain. Treatment of SHP‐1 with a phosphopeptide representing the proximal CD33 ITIM results in increased SHP‐1 enzymatic activity. CD33 exerts an inhibitory effect on tyrosine phosphorylation and Ca2+ mobilization when co‐engaged with the activating FcγRI receptor. This data indicates that CD33 is an inhibitory receptor that may regulate FcγRI signal transduction.