Miracle-dz/UniFAR-FTUs huggingface dataset:
Criticality as a measure of developing proteinopathy in engineered human neural networks

A patterned spread of proteinopathy represents a common characteristic of many neurodegenerative diseases. In Parkinson’s disease (PD), misfolded forms of alpha-synuclein proteins aggregate and accumulate in hallmark pathological inclusions termed Lewy bodies and Lewy neurites, which seems to affect selectively vulnerable neuronal populations and propagate within interconnected neuronal networks. Research findings suggest that these proteinopathic inclusions are present at very early timepoints in disease development, even before strong behavioural symptoms of dysfunction arise, but that these underlying pathologies might be masked by homeostatic processes working to maintain the function of the degenerating neural circuits. This study investigates whether inducing the PD-related alpha-synuclein pathology in engineered human neural networks can be associated with changes in network function, and particularly with network criticality states. Self-organised criticality represents the critical point between resilience against perturbation and adaptational flexibility, which appears to be a functional trait in self-organising neural networks, both in vitro and in vivo. By monitoring the developing neural network activity through the use of multielectrode arrays (MEAs) for a period of three weeks following proteinopathy induction, we show that although this developing pathology is not clearly manifest in standard measurements of network function, it may be discerned by differences in network criticality states.
Direct PA-binding by Chm7 is required for nuclear envelope surveillance at herniations

Mechanisms that control nuclear membrane remodeling are essential to maintain the integrity of the nucleus but remain to be fully defined. Here, we identify a phosphatidic acid (PA)-binding activity in the nuclear envelope-specific ESCRT, Chm7, in budding yeast. PA-binding is mediated through a conserved hydrophobic stretch of amino acids, which confers specific binding to the inner nuclear membrane (INM). This INM-binding is independent but nonetheless required for interaction with the LAP2-emerin-MAN1 (LEM) domain protein, Heh1 (LEM2). Consistent with the functional importance of PA-binding, mutation of this region inhibits recruitment of Chm7 to the INM and abolishes Chm7 function in the context of nuclear envelope herniations or “blebs” that form during defective nuclear pore complex (NPC) biogenesis. In fact, we show that PA accumulates at nuclear envelope herniations. We suggest that local control of PA metabolism is important for ensuring productive nuclear envelope remodeling and that its dysregulation may contribute to pathologies associated with defective NPC assembly.
In pursuit of open science, open access is not enough

Preventing monopolies in knowledge infrastructure is the next battleground for publishers and research institutions After decades of debate on the feasibility of open access (OA) to scientific publications, we may be nearing a tipping point. A number of recent developments, such as Plan S, suggest that OA upon publication could become the default in the sciences within the next several years. Despite uncertainty about the long-term sustainability of OA models, many publishers who had been reluctant to abandon the subscription business model are showing openness to OA (1). Although more OA can mean more immediate, global access to scholarship, there remains a need for practical, sustainable models, for careful analysis of the consequences of business model choices, and for “caution in responding to passionate calls for a ‘default to open’” (2). Of particular concern for the academic community, as subscription revenues decline in the transition to OA and some publishers prioritize other sources of revenue, is the growing ownership of data analytics, hosting, and portal services by large scholarly publishers. This may enhance publishers' ability to lock in institutional customers through combined offerings that condition open access to journals upon purchase of other services. Even if such “bundled” arrangements have a near-term benefit of increasing openly licensed scholarship, they may run counter to long-term interests of the academic community by reducing competition and the diversity of service offerings. The healthy functioning of the academic community, including fair terms and conditions from commercial partners, requires that the global marketplace for data analytics and knowledge infrastructure be kept open to real competition.
The relationship between fen vegetation gradients groundwater flow and flooding in an undrained valley mire at biebrza, Poland

(1) Relationships between vegetation composition and nutrient and major ion concentrations in groundwater and peat were examined in 58 stands of fen vegetation in the Biebrza mire, Poland. The 58 stands included rich fens with a large standing biomass, rich fens with lower standing biomass and poor fens. (2) The highly productive rich fen (i.e. rich fen with large standing biomass) receives moderately eutrophic river water. The rheophilous part of the mire that is not, or only occasionally flooded contains gradients from quite productive rich fens to less productive rich fens and poor fens. In this part of the gradient, occasional river flooding appeared to be an important source of K and was probably responsible for the presence of quite productive rich fen vegetation. (3) Upward seepage of calcium-rich and phosphate-poor groundwater keeps phosphate concentration low in the superficial mire water and the peat from the lower productive rich fen. Phosphate concentration is higher in the mire water and the peat from the poor fen which is fed by downward-flowing rainwater. (4) Nitrogen concentration in mire water and peat is only poorly correlated with species composition and vegetation structure.
Application of fungicides and urea for control of ash dieback

Abstract: Ash dieback is caused by a highly pathogenic fungus Hymenoscyphus pseudoalbidus (anamorph Chalara fraxinea). Possibilities for disease control are limited, and treatment of fallen leaf debris to prevent sporulation of the pathogen is one of the possible options to control the disease. In some cases chemical treatments could be used, but data on effective chemical agents for control of the ash dieback are lacking. The purpose of this study was to examine the effect of different chemical fungicides and urea on the pathogen. Out of eight tested fungicides, mycelial growth in Petri plates as well as development of H. pseudoalbidus apothecia on ash leaf petioles were most efficiently inhibited by carbendazim. Urea also proved to be effective in prevention of apothecial formation. In addition to inhibition of the pathogen, urea accelerates the degradation of treated leaf debris. Therefore, the use of urea for treatment of infected ash leaf debris could be more effective than the use of fungicides and also more environmentally acceptable.
Hybrid Seed Production of Radish (Raphanus sativus L.)

ABSTRACT During recent years, a number of F1 hybrids have been developed in radish by public and private agencies across the world, due to the increasing craze for F1 hybrids. India is not far behind in the race. F1 hybrids have been found advantageous for earliness, high early and total yield, root quality, uniform root development, delayed pithiness, resistance to insect pests, disease and wider adaptability. Sungro Seeds, a leading company in the breeding and production of F1 vegetable bras-sicas in the country, has developed three F1 hybrids in radish in recent years to fulfill the unique needs of the consumers in the country. Before the release of these hybrids, all the radish hybrids marketed in India were imported seeds, mainly from Japan and Korea. In India, the F1 hybrid radish currently shares only 1% of the total seed requirement for radish. However, the trend of using F1 seed is increasing every year. Therefore, there is great latitude for the development of F1 hybrids in radish. The indigenously developed and produced F1 hybrid seed will be available to the farmers on a very competitive rate too.
An Ultrastructural Study of the Feeding Apparatus of Peranema trichophorum

SYNOPSIS A model of the feeding apparatus of Peranema trichophorum Ehrenberg has been constructed from electronmicrographs. A common opening leads via a short anterior canal to the reservoir and cytostome. The cytostome lies close to the internal opening of the canal, and can be moved forward during feeding, closing the passage to the reservoir, and displacing the flagella. The cytostome is supported by the rodorgan in its floor and a double serrated marginal lamella arching over its upper rim from dense bodies lying lateral to the cytostome. A working hypothesis for the movement of the feeding apparatus is proposed. The elaborate system of articulating lamellae operates through these dense bodies which may act as “hinge joints. ” The rodorgan is pulled forward by contraction of longitudinal lamellae attached near the bases of the rods. Cytoplasmic pressure may also be involved. It is suggested that the pull is transmitted through the dense bodies and 2 anchoring lamellae to crescentic canal thickenings on either side of the canal opening. The cytostome, rodorgan and double serrated marginal lamella move forward to fill the external opening of the canal, now enlarged by sideways pull from the anchoring lamellae. Withdrawal of these structures sucks food into the cytostomal sac to be packed down by contraction of the double serrated lamella. It is postulated that the rodorgan operates through adhesion and cytolysis and is not adapted for piercing. A conspicuous striated fibril and associated groups of microtubules in the left wall of the reservoir are cytoskeletal structures.
The Neuronal Microtubule‐Associated Protein Tau Is a Substrate for Caspase‐3 and an Effector of Apoptosis

We have identified a class of tau fragments inducing apoptosis in different cellular contexts, including a human teratocarcinoma‐derived cell line (NT2 cells) representing committed human neuronal precursors. We have found a transition point inside the tau molecule beyond which the fragments lose their ability to induce apoptosis. This transition point is located around one of the putative caspase‐3 cleavage sites. This is the only site that can be effectively used by caspase‐3 in vitro, releasing the C‐terminal 19 amino acids of tau. These results establish tau as a substrate for an apoptotic protease that turns tau itself into an effector of apoptosis. Accordingly, tau may be involved in a self‐propagating process like what has been predicted for the pathogenesis of different neurodegenerative disorders.
CULTIVATED Helianthus annuus DIFFERS FROM TWO WILD RELATIVES IN GERMINATION RESPONSE TO SIMULATED DROUGHT STRESS

SUMMARY Wild sunflowers are a source of desirable traits for improving cultivated sunflower Helianthus annuus (ANN). Two wild species of sunflower, H. argophyllus (ARG) native to coastal sand dunes and H. niveus ssp. tephrodes (TEPH) native to the desert sand dunes, have been hypothesized to be drought resistant. We tested the expectation that these wild species would have higher percent germination and more uniform germination under simulated drought stress conditions compared to cultivated ANN. In a growth chamber study, we assessed germination of ANN, ARG and TEPH (three representative accessions for each species) under four osmotic stress treatments imposed using polyethylene glycol to simulate varying levels of drought stress: 0, -0.4, -0.8 and -1.2 MPa. As expected, all three species responded to increasing simulated drought stress with decreased percent germination assessed after seven days and delayed germination timing and uniformity assessed with logistic regressions. ARG responded marginally better than ANN with a greater percent germination at -1.2 MPa and greater uniformity at 0 and -0.4 MPa. Although the ARG advantage was small, this suggests that ARG × ANN recombinant hybrids may deserve further investigation to see if desirable alleles can be identified for improving cultivated ANN germination and establishment under mild drought conditions. In contrast, TEPH responded with substantially lower percent germination and less uniformity than ANN, suggesting that it is unlikely that TEPH will be useful as a donor of desirable drought resistance alleles.
Amphiroa currae (Corallinaceae), a new species of marine algae from Venezuela1,,2

Abstract A new epiphytic Amphiroa, A. currae (Corallinaceae, Rhodophyta) is described from Venezuela. The plants form tiny cushions, 0.5–1.5 cm in diameter, on Gelidium serrulatum J. Ag. The articulated portion comprises fewer than sixteen intergenicula. Conceptacles occur both in the crustose and segmented portions.
Error profiles for Next Generation sequencing technologies

Next generation sequencing has revolutionized genome research and marked the start of a new era. These technologies present us with unprecedented amounts of data - but with this sequencing data comes errors that are not only platform specific but also depend on the library preparation method and the type of sequencing (i.e. amplicon or metagenome). Illumina’s sequencing platforms are currently among the most utilized platforms as they are able to generate millions of reads at relatively low cost – but Illumina error profiles are still poorly understood. A better knowledge of the error profiles is essential for sequence analysis and vital in order to draw valid conclusions. It has been reported that the major source of errors for Illumina are substitution-type miscalls. We developed a program that enables us to infer error profiles based on sequencing data from mock communities. This allows us to study and compare different errors and biases introduced by different sequencing machines, different library preparation methods as well as different types of sequencing. Here, we present the metagenome error profiles for a mock community that was sequenced on the Genome Analyzer (GA) II for the standard Illumina library preparation method (TruSeq). Being able to infer error profiles for individual sequencing runs has the potential to greatly improve our ability to correct errors and thus enhance further sequencing analysis.
Morphological traits determine specialization and resource use in plant–hummingbird networks in the neotropics

Ecological communities are organized in complex ecological networks. Trait-based analyses of the structure of these networks in highly diversified species assemblages are crucial for improving our understanding of the ecological and evolutionary processes causing specialization in mutualistic networks. In this study, we assessed the importance of morphological traits for structuring plant–hummingbird networks in Neotropical forests by using a novel combination of quantitative analytical approaches. We recorded the visitation of hummingbirds to plant species over an entire year at three different elevations in Costa Rica and constructed quantitative networks based on interaction frequencies. Three morphological traits were measured in hummingbirds (bill length, bill curvature, and body mass) and plants (corolla length, curvature, and volume). We tested the effects of avian morphological traits and abundance on ecological specialization of hummingbird species. All three morphological traits of hummingbirds .
Emulating Riverine Landscape Controls of Beaver in Stream Restoration

ABSTRACT Stream and floodplain restoration at the reach scale has ranged from expensive, heavy-handed modification of the channel and floodplain to simple, longer-term revegetation efforts. We have developed and implemented a simple approach that emulates the ecosystem engineering effects of beaver. This approach is less expensive and disruptive than typical large-scale engineering efforts and has the potential to restore both fish habitat and floodplain vegetation more rapidly than simply revegetating and waiting for the riparian zone to mature. The approach involves constructing log flow-choke structures that mimic the hydraulic function of a natural beaver dam during flooding. By placing these structures throughout a naturally entrenched stream reach at locations promoting increased frequency of flood connection with floodplain swales and relict channels, we set the stage to restore the riparian corridor and floodplain more quickly than could be achieved through revegetation alone. Monitoring shows tha.
Augmentation of aripiprazole by flupenthixol decanoate in poorly responsive schizophrenia: a randomized clinical study

ABSTRACT OBJECTIVE: According to some studies, while first-generation antipsychotics were associated with slightly better outcomes and lower costs in comparison with second-generation antipsychotics, atypical antipsychotics have become the most commonly used class of antipsychotic drugs in clinical practice. The objective of this study was to examine whether there could be any positive outcome if flupenthixol decanoate was added, as an adjuvant, to aripiprazole in poorly responsive cases of schizophrenia. METHODS: Twenty-four male inpatients with diagnosis of schizophrenia, according to the DSM-5 diagnostic criteria, who had shown poor response to aripiprazole, were entered into an eight-week, parallel group, single-blind study for random assignment to either aripiprazole plus augmentative flupenthixol decanoate or current antipsychotic treatment in a 1:1 ratio. Primary outcome measures of the study were changes in the mean total scores of the Scale for Assessment of Positive Symptoms (SAPS) and the Scale for Assessment of Negative Symptoms (SANS). The secondary measures were the Schedule for Assessment of Insight (SAI), the Clinical Global Impressions-Severity Scale (CGI-S), and the Simpson-Angus Scale (SAS). RESULTS: According to the findings, the mean total scores of SAPS, SAI, and CGI-S in the augmented group decreased significantly in comparison with the aripiprazole group (p < .01, p < .05, p < .01 , respectively), with around 19.55% decrement of SAPS in the augmented group. Conversely, the reduction in the mean total score of SANS was not significant in between-group analysis (p > .05). Also, the mean total score of SAS was significantly increased in the augmented group (p < .01). The effect-size analysis showed a large improvement with flupenthixol augmentation in terms of SAPS, SAI, and CGI-S scores. CONCLUSIONS: While emergence of extra-pyramidal side effects should not be overlooked by clinicians, adding flupenthixol decanoate to aripiprazole may be beneficial for some cases of poorly responsive schizophrenia.
The Extent to which Government Housing Programs Meet the Expectations of Intended Beneficiaries in South Africa

Abstract Although numerous housing projects for the needy have been established in South Africa since 1994, many reports show their inadequacy in meeting the expectations of the intended beneficiaries. It is based on thisnotion that this paper was crafted to explore the extent to which housing programs meet the expectations of intended beneficiaries. The study collected data from 276 samples or participants who were subjected to eitherinterviews or questionnaires. The findings show that the beneficiaries were not happy with the quality, size andspacing of the houses, the intended beneficiaries felt that the distance of the houses to other socio-economiclocations such as schools, hospitals and police were very far, and the government and contractors’ slow pace ofconstruction of the houses was disturbing and very slow. The researchers recommend an overhaul in theimplementation of the housing program to ensure that the expectations of the intended beneficiaries are met.Thorough monitoring and evaluation is needed to promote and strengthen accountability at all levels. This paperis derived from a broader research study that sought to investigate the implementation of housing programstowards addressing housing problems in the Amathole district of the Eastern Cape Province with the objective ofthis study being to investigate and establish the extent to which the housing projects meet the expectations of thetargeted beneficiaries in South Africa.
Identification of predators using a novel photographic tethering device

Tethering prey is often used to help determine the impact of predators in aquatic communities. In this study, a novel photographic tethering device was used to make digital recordings of predation events on juveniles of the spiny lobster, Jasus edwardsii. Predation of lobsters was significantly higher during the day (76%) than at night (33.4%). This was consistent with a SCUBA survey that found greater numbers of diurnal predators than nocturnal predators at the study site. However, the abundance of predators was not consistent with the number of predation events for individual species as recorded by the photographic tethering device. The snapper, Pagrus auratus, was the most abundant species at the study site (45% of all diurnally active fishes), but was only responsible for 12% of predation events during the day. In contrast, wrasse species were responsible for the greatest number of predation events during the day (60%), yet made up only a small proportion of the diurnal fish population (25%). The results of this study indicate the importance of determining the identity of potential predators, through the use of a photographic tethering device, for increasing the value of results generated from tethering experiments.
Documentation

Document Number 1, Remarks by President George W. Bush on Weapons of Mass Destruction Proliferation, Fort Lesley J. McNair, National Defense University, Washington, D.C., February 11, 2004 Document Number 2, Prepared Testimony of Lieutenant General Ronald T. Kadish, Director, Missile Defense Agency, on the Missile Defense Program and Fiscal Year 2005 Budget before the Senate Armed Services Committee, March 11, 2004 Document Number 3, Prepared Statement of Ambassador Linton F. Brooks, Under Secretary of Energy for Nuclear Security and Administrator, National Nuclear Security Administration, before the Senate Armed Services Committee, Subcommittee on Strategic Forces, 24 March 2004
The Chemical Nature of an Antiviral Factor (AVF) from Virus-infected Plants

Summary An antiviral factor from virus-infected plants (AVF) was purified in an active form on SDS-polyacrylamide gels. AVF binds to concanavalin A and is partially sensitive to α-glucosidase. It is sensitive to pronase only when incubated in conditions suitable for proteolysis of glycoproteins. Alkaline phosphatase affected the electrophoretic mobility of AVF, but did not abolish antiviral activity. AVF was insensitive to DNase, β-glucosidase and pancreatic lipase. The AVF band obtained upon electrophoresis could be stained with Coomassie blue and by the Schiff-periodate procedure for carbohydrates. AVF is considered to be a phosphoglycoprotein with a mol. wt. of about 22000.