Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduced-nutrient leachates in cash cover crop-soybean systems

Over-wintering crops are known to reduce nutrients in soil leachate in spring, but little economic incentive is available to grow these crops in the Upper Midwest. New oilseed-bearing cash cover crops, such as winter camelina and pennycress, may provide the needed incentives. However, the abilities of these crops to sequester labile soil nutrients are unknown. We used lysimeters buried at 30, 60, and 100 cm to examine nitrate and soil reactive phosphorus (SRP) in six soybean cropping system treatments: clean till, no-till, and autumn-seeded radish, winter rye, pennycress, and winter camelina. Radish winter-killed naturally, winter rye was killed with a glyphosate, and pennycress and winter camelina were allowed to mature naturally after relay sowing of soybean. Leachate chemistry was studied for the autumn, spring, and summer periods over two growing season. In autumn, leachates under radish and winter rye tended to have the lowest nitrate levels. In spring, differences among nitrate levels across treatments were greater than at any other time period, with values much lower under pennycress and winter camelina treatments than other treatments. In summer, nitrate levels were more uniform, with the lowest values occurring where soybean grew best. In general, cash cover crops like pennycress and winter camelina provide both environmental and economic resources to growers in that they represent cash-generating grain crops that sequester labile soil nutrients, especially in spring, and protect and promote soil health from autumn through early summer.
Effects of the GTPase Rab31 on breast cancer cell proliferation, adhesion, and expression of other tumor-associated genes

The data presented provide novel insights into cell biological and molecular changes triggered by overexpression or repression of the GTPase Rab31 (or mutants thereof) in breast cancer cells. Repression of TGF-b1 production - as well as up-/down-regulation of several other factors of the (non-)canonical TGF-b signaling pathways - may elicit the change of the cell biological phenotype (e.g. increased proliferation and decreased adhesion) of breast cancer cells upon Rab31 overexpression.
Bacterial diversity of the abandoned mamut copper mine in Sabah, Malaysia and its correlation with copper contamination

: The former Mamut Copper Mine, acid mine drainage site represents an anthropogenic altered landscape characterized by its acidic topsoil which is contaminated primarily with copper. Even though the mining operation was ceased at 1999, the bacterial diversity in this area has never been investigated. This study was conducted to ascertain the bacterial diversity of this abandoned copper mine and correlate it to the copper concentration in the soil. Methodology and results: Soil samples were collected from 7 sites near the mine pit and the vicinity. Soil samples were assessed for soil copper elemental concentration using inductively coupled plasma optical emission spectrometry and bacteria were isolated via serial dilution followed by culture on nutrient agar plates. Phylogenetic analysis was done based on the full-length sequences of 16S rRNA gene. Twenty-four phylotypes were obtained from the 7 locations which originated from the phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The results of the study indicated that site 2 (6.030223°; 116.658030°), located in between the mine pit and the mine factory with a copper concentration of 88.96 ppm, possessed the most diverse bacterial community with a Shannon diversity index (H) of 1.68, evenness (EH) of 0.94 and richness (S) of 6. Conclusion, significance and impact of study: Current study revealed that there was a positive correlation between the copper concentration and the H index and the richness, but this was not reflected in the evenness. This is the first report of bacterial diversity from the former Mamut Copper Mine site. The data provided a valuable insight for the future monitoring of the bacterial community in this ecologically important niche.
Atomic model of microtubule-bound tau

Tau is a developmentally regulated protein found in axons, whose physiological role is to stabilize and bundle microtubules (MTs). Hyper-phosphorylation of tau is thought to cause its detachment from MTs and subsequent aggregation into pathological fibrils that have been implicated in Alzheimer’s disease pathogenesis. Despite its known MT binding role, there is no consensus regarding which tau residues are crucial for tau-MT interactions, where on the MT tau binds, and how binding results in MT stabilization. We have used cryo-EM to visualize the interaction of different tau constructs with MTs at high resolution (3.2-4.8 Å) and used computational approaches to generate atomic models of tau-tubulin interactions. Our work shows that the highly conserved tubulin-binding repeats within tau adopt very similar structures in their interactions with the MT. Each tau repeat binds the MT exterior and adopts an extended structure along the crest of the protofilament (PF), interacting with both α- and β-tubulin, thus stabilizing the interface between tubulin dimers. Our structures agree with and explain previous biochemical data concerning the effect of phosphorylation on MT affinity and lead to a model in which tau repeats bind in tandem along a PF, tethering together tubulin dimers and stabilizing longitudinal polymerization interfaces. These structural findings could establish a basis of future treatments aiming at the selective stabilization of tau-MT interactions.
Applying the Water-Energy Nexus for Water Supply—A Diagnostic Review on Energy Use for Water Provision in Africa

This work explores the application of the Water-Energy Nexus concept for water supply in the African context, where its operationalization is quite limited compared to developed regions. Furthermore, water supply and demand drivers and their influence on energy use are examined. This study found that there is limited literature available on the operationalization of the concept, and energy use is not considered a key performance indicator by water regulators and utilities. Regionally, most of the studies were carried out in the northern and southern Africa, where energy demand for water supply through desalination is high. An analysis of water supply and demand drivers show diminishing quantities of available freshwater, and increased anthropogenic pollutant loads in some areas are projected. Consequently, utilities will likely consider alternative energy-intensive water supply options. Increased population growth with the highest global urban growth rate is projected, with about 60% of the total population in Africa as urban dwellers by 2050. This implies huge growth in water demand that calls for investment in technology, infrastructure, and improved understanding of energy use and optimization, as the largest controllable input within utilities boundaries. However, it requires a data-driven understanding of the operational drivers for water supply and incorporation of energy assessment metrics to inform water-energy policies and to exploit the nexus opportunities.
Reflections on a Career as an Industrial Organization and International Economist

In this article, I reflect on my career in the agricultural economics profession as a researcher who has focused predominantly on the synthesis of two fields in economics: industrial organization and international trade. In that context, I consider my main contribution to have been in analyzing the impact of public policy where imperfect competition matters in the food and agricultural marketing system, be it in either the horizontal or vertical market dimensions. In addition, I have also paid considerable attention to incorporating market structure into empirical analysis of food and agricultural trade.
Isolation and Characterization of Two siamese Phenotypic Modifiers and Their Role in Endoreplication and Trichome Development

Recessive mutations in the ENS1 gene of Arabidopsis thaliana result in reduced trichome branching without altering the ploidy level of trichomes. This implies that ENS1 regulates trichome branching in an endoreplication-independent manner. Mutations in ENS1 also enhance the multicellularity of sim mutant trichomes indicating that ENS1 plays a role in the regulation of the cell cycle during trichome cell differentiation. We have shown that ENS1 is required by the negative regulators of trichome branching for the trichomes to achieve their supernumerary branching. The interaction between ens1-1 and try-JC suggests that ENS1 is involved in both primary and secondary branching events during trichome development. The ENS1 protein interacts both genetically and physically with the STI protein and double mutant analysis between ens1-1 and sti mutants revealed that they function in the same pathway during trichome development. We propose that ENS1 and STI form a complex that functions to ensure the development of a wild-type trichome phenotype. The ens2-1 mutations result in trichomes with reduced branching and reduced endoreplication. The ens2-1mutations also enhance the multicellularity of sim mutant trichomes. The ENS2 gene encodes an activator of the APC/C, a multisubunit protein complex that targets proteins for degradation by the 26S proteasome. Overexpression of ENS2 and its close Arabidopsis homologue AtCCS52A2 results in plants with retarded growth that have enlarged leaf epidermal pavement cells containing highly endoreplicated nuclei. These plants also have large multibranched trichomes with highly endoreplicated nuclei. Both ENS2 and AtCCS52A2 suppress the sim mutant trichome
Liegeverhalten von Pferden in Gruppenauslaufhaltung

Abstract. Titel of the paper: Recumbence resting behaviour of horses in loose housing Systems with open yards Recumbence resting behaviour was investigated in 48 horses in four loose housing Systems with open yards subdivided in areas for feeding, recumbence and for free range. Continuous observations were made for each loose housing system on three independent days during a 24-hr period. In all housing Systems the horses chose exclusively the area of recumbence to rest in sternal or lateral position. On the one hand the dimension of the area of recumbence influenced we recumbence resting behaviour. In the fourth housing system the insufftcient recumbence area reduced the resting time. At the other hand the time of recumbence was dependent on social rank. The animals with lower rank showed a significant shorter recumbence time than the horses with higher rank. However the frequency of recumbence was similar in all horses independent of stable, social rank and age. The results clearly show, that the dimension of the area of recumbence as the only parameter is not enough to satisfy the demand of recumbence in all horses.
Communicative Governance to Mitigate the COVID-19 Pandemic

Emerging democracies are handicapped by systemic weaknesses such as inadequate healthcare safety nets, weak administrative capacities, and rigidly hierarchical bureaucracies and conflicts between levels of political leadership. The COVID-19 pandemic creates the urgent need for governments to overcome these structural limitations and facilitate responsive governance. This article uses the lens of communicative governance to describe how governments respond to the emerging health emergency and its challenges. It uses the case of the state of Delhi in India to analyze how the tools of government were operated to govern during an escalating health crisis. It documents the unique policy and administrative practices that are driving the response to the COVID-19 pandemic in the global South. In doing so, it points to the ways in which urban e-planning can foster transformative capacities to support local communities.
A Coherent Spurious Analysis for Sub-THz Frequency Multiplier Chains

At sub-THz frequencies, the local oscillation for transceivers is often generated by an analog frequency multiplier tree. This paper studies the origins and minimization of spurious tones in a local oscillator multiplier consisting of a chain of frequency doublers. It is found that the nearest spurious components depend on the leakage of the input signal in the first multiplier, which can be minimized by active bias tuning, filtering in the first stage or better balance in the driving differential signal. To verify the nonlinearity modeling, 0.13-μm SiGe BiCMOS technology has been utilized.
Prevalencia del parasitismo gastrointestinal en bovinos del departamento Cesar, Colombia

El objetivo del estudio fue determinar la prevalencia de parasitos gastrointestinales en bovinos del departamento del Cesar, Colombia. Se colectaron 862 muestras fecales en 27 fincas de doble proposito de dos municipios. Los animales fueron estratificados en tres grupos etarios: 0-12, 12-24 y >24 meses. Las muestras se procesaron mediante las tecnicas coprologicas de McMaster, Dennis y Baermann. Se identificaron los generos de los parasitos segun morfologia de sus huevos o larvas infectivas. La prevalencia global de parasitos gastrointestinales fue de 83.2%, siendo los valores mas altos para Eimeria sp (77.9%), Strongyloides sp (10.8%) y Haemonchus sp (8.5%). No se encontro asociacion estadistica por efecto de los municipios, pero se observo por efecto del grupo etario en la prevalencia de Eimeria sp, Strongyloides, Haemonchus y Trichostrongylus (p<0.05).
Effect of early feed restriction on body weight and compensatory growth in Label Rouge broiler chickens

This research was conducted to assess the compensatory gain in birds that have suffered severe food restriction and a reduced growth in its initial phase. A total of 144 birds were used in the Label Rouge lineage with average initial weight 239.90 ± 76.80 g, from 28 to 49 days. The experimental design used was a completely randomized design, where the birds were distributed in 18 boxes, containing 3 treatments and 6 replicates of 8 birds per cage. The treatments were as follows: birds with body weight of 150.73 ± 12.62 g, between weighing from 239.79 ± 13.14 g and heavy weight of 329.17 ± 24.89 g in different periods, from 28 to 35, 35 to 42 and 42 to 49 days of age, respectively. In relation to weight gain, the heavy birds, obtained better results when compared to the other. The feed consumption has changed in the three periods and, in the period of 42 to 49 days, the treatments did not differ among themselves. Feed conversion rates (p = 0.127) and feasibility (p = 0.6163) of birds do not differ in different periods.
Temporal beta diversity of lake plants is determined by concomitant changes in environmental factors across decades

To comprehensively understand the impact of anthropogenic activities on biodiversity, we must understand how biodiversity has changed over time and what are the underlying processes. A growing body of evidence has shown that beta diversity reveals more about temporal changes in biodiversity compared with alpha diversity. Temporal beta diversity indicates, for example, degrees of change in species composition at single locations through time. We examined whether freshwater plant communities showed different patterns in temporal beta diversity in relation to concomitant changes in environmental conditions across decades. To do this, we used presence–absence data of lake plants for five decades (1940s–2010s) from southern Finland and calculated temporal beta diversity indices (TBI) for each lake between pairs of decades to the whole community, hydrophytes and helophytes. To get insights into possible processes behind the observed trends, we decomposed TBIs into beta diversity contributed by either temporal losses or temporal gains of species. We related TBIs and their loss and gain components to lake landscape position and changes in environmental variables. Based on comparisons of TBIs between the survey decade pairs, the temporal change in aquatic plant communities was modest through decades. Hydrophyte assemblages have changed more than helophyte assemblages. The main changes in temporal beta diversity occurred from the 1940s to the 1970s, when the gain of new species was the dominant process in the lakes throughout the landscape. Following that period, there was only modest changes, but from the 2000s to the 2010s, the dominant process was the loss of species. Temporal changes in environmental conditions played a key role in explaining the TBI. Our results showed that relying on only two survey points in time can result in limited knowledge of the ecological phenomenon under study and, for example, an exceptional year in terms of weather conditions can hinder detecting overall long‐term trends in compositional changes. Therefore, future studies should try to combine data from several decades to overcome the typical limitations of temporal information.
Targeting RNA splicing for disease

Splicingofpre-messengerRNAintomaturemessengerRNAisanessentialstepfor the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a numberoftoolsincludingantisenseoligonucleotides,modifiedsmallnuclearRNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expressionresultingfromgenemutationsthataltersplicing.Herewedescribeclinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splicemodulating approaches, and emerging therapeutics.  2013 John Wiley & Sons, Ltd.
Antioxidant Migration Studies in Chitosan Films Incorporated with Plant Extracts

The aim of this work was to develop an active biopolymer based on chitosan by incorporating natural antioxidants. Five essential oils (ginger, rosemary, sage, tea tree and thyme) and six hydro-alcoholic extracts (from ginger, green and black tea, kenaf leaves, rosemary and sage plants) were tested. Migration assays were carried out to evaluate the films’ activity, and total phenolic content and antioxidant activity were monitored in the simulant during storage. Interaction between natural compounds and polymeric matrix was evaluated by FTIR spectroscopy. The diffusion of the phenolic compounds was not detected in the films incorporated with hydro-alcoholic extracts (HAEs), indicating their entrapment in the chitosan. Migration was observed in the films with essential oils (EOs), and biobased films incorporated with ginger, sage or rosemary essential oils, presented the highest diffusion and antioxidant activity in the simulant, highlighting their functionality and potential to be used as food active packaging material.
Extended High Frequency Audiometry for Revealing Sudden Sensory Neural Hearing Loss in Acute Tinnitus Patients

Abstract Introduction The measurement of extended high-frequency (EHF) audiometry has become more popular recently, mainly in connection with ototoxicity and noiseinduced hearing loss. New-onset tinnitus evaluation includes a standard hearing test that shows no pathology. Objective The aim of the present study was to evaluate the possibility that acute tinnitus is essentially connected to sudden sensory neural hearing loss (SSNHL), by utilizing EHF audiometry in cases in which standard audiometry for frequencies between 250 Hz to 8 kHz is within normal limits. Methods A retrospective study was conducted between January 2009 and May 2014 that included all patients presenting with acute tinnitus and normal standard audiometry. All patients underwent EHF audiometry and were treated accordingly. Results Thirty-two patients with acute tinnitus and asymmetric sensorineural hearing loss on EHF audiometry were identified. The average deltas between the ears were between 9.2 and 33dB (worse in the affected ear). Conclusion Extended high-frequency audiometry up to 20,000 Hz should be performed in all patients with acute tinnitus and standard audiometry within normal limits.
Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi

Anopheles stephensi is a potent vector of malaria throughout the Indian subcontinent and Middle East. An. stephensi is emerging as a model for molecular and genetic studies of mosquito-parasite interactions. Here we conducted a series of genomic and transcriptomic studies to improve the understanding of the biology of Anopheles stephensi and mosquito in general. First we reported the genome sequence and annotation of the Indian strain of the “type” form of An. stephensi. The 221 Mb genome assembly was produced using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than assemblies generated from a single data source. A total of 11,789 protein-encoding genes were annotated using a combination of homology and de novo prediction. Secondly, we demonstrated the presence of complete dosage compensation in An. stephensi by determining that autosomal and X-linked genes have very similar levels of expression in both males and females. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the conclusion of complete dosage compensation in Anopheles. Lastly, we investigated trans-splicing events in Anopheles stephensi. We identified six transsplicing events and all the trans-splicing sites are conserved and present in Ae. aegypti. The proteins encoded by the trans-spliced mRNAs are also highly conserved and their orthologs are co-linearly transcribed in out-groups of family Culicidae. This finding indicates the need to preserve the intact mRNA and protein function of the broken-up genes by trans-splicing during evolution. In summary, we presented the first genome assembly of Anopheles stephensi and studied two interesting evolution events – dosage compensation and trans-splicing via transcriptomic analysis. Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi Xiaofang Jiang