Miracle-dz/UniFAR-FTUs huggingface dataset:
Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression

Sperm small RNAs have emerged as important non-genetic contributors to embryogenesis and offspring health. A subset of sperm small RNAs are thought to be acquired during epididymal transit. However, the transfer of RNAs from the somatic epididymis to sperm has been questioned, and the identity of the specific small RNAs transferred remains unclear. Here, we employ Cre/Lox genetics to generate germline- and epididymal-specific Dgcr8 conditional knockout mice to investigate the dynamics of sperm microRNAs and their function in the early embryo. Testicular sperm from germline specific Dgcr8 knockout mice have reduced levels of 98 microRNAs. Enthrallingly, following epididymal transit the abundance of 59% of these microRNAs are restored to control levels. Conversely, sperm from epididymal Dgcr8 knockouts displayed a reduction of > 3.4-fold in 25 miRNAs. This substantial loss of epididymal miRNAs in sperm was accompanied by transcriptomic changes in the embryo which was rescued by microinjection of epididymal miRNAs. These findings ultimately demonstrate the acquisition of miRNAs from the soma by sperm during epididymal transit and their subsequent regulation of post-fertilization embryonic gene expression.
A Masking Protocol for Private Communication and Attack Detection in Nonlinear Observers

This work presents a novel masking protocol to secure the communication between a nonlinear plant and a non-linear observer. Communication is secured in two senses. First, the privacy of the plant is preserved during the communication. Second, the protocol can detect a false-data injection attack in the communication link. The masking protocol is based on the use of washout-filters in nonlinear observers and the internal model principle.
Package ‘comparator’

October 12, 2022 Type Package Title Comparison Functions for Clustering and Record Linkage Version 0.1. 2 Date 2022-03-15 Maintainer Neil Marchant <ngmarchant@gmail.com> Description Implements functions for comparing strings, sequences and numeric vectors for clustering and record linkage applications. Supported comparison functions include: generalized edit distances for comparing sequences/strings, Monge-Elkan similarity for fuzzy comparison of token sets, and L-p distances for comparing numeric vectors. Where possible, comparison functions are implemented in C/C++ to ensure good performance. License GPL (>= 2) Imports Rcpp (>= 1.0.5), proxy (>= 0.4), methods, clue (>= 0.3) LinkingTo Rcpp RoxygenNote 7.1. 2 Encoding UTF-8 URL https://github.com/ngmarchant/comparator BugReports https://github.com/ngmarchant/comparator/issues Collate 'Comparator.R' 'CppSeqComparator.R' 'PairwiseMatrix.R' 'SequenceComparator.R' 'StringComparator.R' 'BinaryComp.R' 'NumericComparator.R' 'Chebyshev.R' 'Constant.R' 'Levenshtein.R' 'DamerauLevenshtein.R' 'Minkowski.R' 'Euclidean.R' 'FuzzyTokenSet.R' 'Hamming.R' 'InVocabulary.R' 'Jaro.R' 'JaroWinkler.R' 'LCS.R' 'Lookup.R' 'Manhattan.R' 'TokenComparator.R' 'MongeElkan.R' 'OSA.R' 'RcppExports.R' 'generalized_mean. R' 'strcompr-package.R' 'util.R' Suggests testthat NeedsCompilation yes Author Neil Marchant [aut, cre] Repository CRAN Date/Publication 2022-03-16 09:20:02 UTC
Word and Nonword Reading Efficiency in Postlingually Deafened Adult Cochlear Implant Users

Hypothesis: This study tested the hypotheses that 1) experienced adult cochlear implants (CI) users demonstrate poorer reading efficiency relative to normal-hearing controls, 2) reading efficiency reflects basic, underlying neurocognitive skills, and 3) reading efficiency relates to speech recognition outcomes in CI users. Background: Weak phonological processing skills have been associated with poor speech recognition outcomes in postlingually deaf adult CI users. Phonological processing can be captured in nonauditory measures of reading efficiency, which may have wide use in patients with hearing loss. This study examined reading efficiency in adults CI users, and its relation to speech recognition outcomes. Methods: Forty-eight experienced, postlingually deaf adult CI users (ECIs) and 43 older age-matched peers with age-normal hearing (ONHs) completed the Test of Word Reading Efficiency (TOWRE-2), which measures word and nonword reading efficiency. Participants also completed a battery of nonauditory neurocognitive measures and auditory sentence recognition tasks. Results: ECIs and ONHs did not differ in word (ECIs: M = 78.2, SD = 11.4; ONHs: M = 83.3, SD = 10.2) or nonword reading efficiency (ECIs: M = 42.0, SD = 11.2; ONHs: M = 43.7, SD = 10.3). For ECIs, both scores were related to untimed word reading with moderate to strong effect sizes (r = 0.43–0.69), but demonstrated differing relations with other nonauditory neurocognitive measures with weak to moderate effect sizes (word: r = 0.11–0.44; nonword: r = (−)0.15 to (−)0.42). Word reading efficiency was moderately related to sentence recognition outcomes in ECIs (r = 0.36–0.40). Conclusion: Findings suggest that postlingually deaf adult CI users demonstrate neither impaired word nor nonword reading efficiency, and these measures reflect different underlying mechanisms involved in language processing. The relation between sentence recognition and word reading efficiency, a measure of lexical access speed, suggests that this measure may be useful for explaining outcome variability in adult CI users.
Long-term ozone trends at rural ozone monitoring sites across the United States, 1990-2010

[1] This analysis provides an up-to-date assessment of long-term (1990–2010) rural ozone trends using all available data in the western (12 sites) and eastern (41 sites) USA. Rather than focus solely on average ozone values or air quality standard violations, we consider the full range of ozone values, reporting trends for the 5th, 50th and 95th percentiles. Domestic ozone precursor emissions decreased strongly during 1990–2010. Accordingly 83%, 66% and 20% of summertime eastern U.S. sites experienced statistically significant ozone decreases in the 95th, 50th and 5th percentiles, respectively. During spring 43% of the eastern sites have statistically significant ozone decreases for the 95th percentile with no sites showing a significant increase. At the 50th percentile there is little overall change in the eastern U.S. In contrast, only 17% (2 sites) and 8% (1 site) of summertime western U.S. sites have statistically significant ozone decreases in the 95th and 50th percentiles, respectively. During spring no western site has a significant decrease, while 50% have a significant median increase. This dichotomy in U.S. ozone trends is discussed in terms of changing anthropogenic and biomass burning emissions. Consideration is given to the concept that increasing baseline ozone flowing into the western U.S. is counteracting ozone reductions due to domestic emission reductions. An update to the springtime free tropospheric ozone trend above western North America shows that ozone has increased significantly from 1995 to 2011 at the rate of 0.41 ± 0.27 ppbv yr−1. Finally, the ozone changes are examined in relation to regional temperature trends.
Proteinase-Activated Receptor 4 (PAR4) Activation Triggers Cell Membrane Blebbing through RhoA and β-arrestin

Proteinase-Activated Receptors (PARs) are a four-member family of G-protein coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by serine proteinases such as thrombin, trypsin and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types including platelets, vascular smooth muscle cells and neuronal cells. In studying PAR4 signalling and trafficking, we observed dynamic changes in the cell membrane with spherical membrane protrusions that resemble plasma membrane blebbing. Since non-apoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release we sought to elucidate the signalling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/Cas9-mediated gene-editing approaches we establish that PAR4-dependent membrane blebbing occurs independently of the Gαq/11 and Gαi signalling pathways and is dependent on signalling via the β-arrestin-1/-2 and RhoA signalling pathways. In order to gain a more comprehensive understanding of β-arrestin-mediated signalling downstream of PAR4 and to guide future studies, we undertook RNA-seq analysis of PAR4 activated genes in control cells and in cells lacking β-arrestin-1/-2. A list of differentially expressed genes was generated followed by Gene Ontology (GO) and enrichment analysis, revealing PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission-terms that relate back to known functions of PAR4 and are consistent with our finding of membrane blebbing triggered by PAR4 activation. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function. Significance Statement We find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA- and β-arrestin-dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4. Finally through CRISPR/Cas9-mediated targeting and RNA-seq analysis we catalogue here PAR4-dependent transcription that is dependent on β-arrestin.
Correlation between smoke and tropospheric ozone concentration in Cuiabá during Smoke, Clouds, and Radiation‐Brazil (SCAR‐B)

Ozone soundings launched from Cuiaba between August 16 and September 10, 1995, during the Smoke, Clouds, and Radiation-Brazil (SCAR-B) experiment show an enrichment of tropospheric ozone when compared with average wet season values and also present a great variability in concentrations depending on the dominant circulation pattern. Smoke tracers, such as aerosol optical thickness, measured from a Sun photometer installed at the Instituto Nacional de Pesquisas Espaciais-Cuiaba site, and black carbon ground measurements, also show an enhancement of smoke during the same period. Although there is a connection between the enrichment of the tropospheric ozone around Cuiaba during the dry season and smoke from biomass burning, the correlation between ozone and smoke indicates different behavior in different periods. Trajectory analyses suggest that the strong ozone peak measured in the period between August 26 and 29, 1995, may be associated not only with direct biomass-burning emissions but also with urban/industrial emissions from big cities on the coast of Brazil and recirculation of old smoke. This view is confirmed by measurements made from the Cloud Lidar System instrument aboard the ER-2 aircraft.
Global Relationship between Fronts and Warm Conveyor Belts and the Impact on Extreme Precipitation

AbstractExtratropical cyclones are responsible for many extreme precipitation events in the midlatitudes. Warm conveyor belts (WCBs) and fronts are known to be related to the uplift and hence the precipitation within cyclones. The authors have investigated the link between WCBs and fronts and how such a link impacts the occurrence of extreme precipitation events. WCB trajectories have been calculated from the ERA-Interim dataset, and low-level (below 790 hPa) and midlevel (790–600 hPa) WCBs have been considered. These have been matched with objectively identified fronts (i.e., characterized by an overlap of WCB and front somewhere along the front). About 10% of cold fronts, 8% of warm fronts (identified using a thermal criterion), and 15% of wind fronts (identified using a wind shift method) are matched with WCBs, while up to 70% of WCBs are matched with fronts. Some WCBs, especially in the Southern Hemisphere, are not matched with either type of front (up to 70% east of Australia). The relationship betwe.
3. Nutritional enrichment of broiler breast meat through dietary supplementation of Indian ginseng Withania somnifera and synbiotic substances under semi-arid climatic conditions

Aim: The objective of this research was to determine the species and strains of Leucocytozoon caulleryi and study the phylogenetics of L. caulleryi of broiler chickens in endemic areas in Indonesia. Materials and Methods: Blood samples were collected from broiler chickens originated from endemic area in Indonesia, i.e., Pasuruan, Lamongan, Blitar, Lumajang, Boyolali, Purwokerto, and Banjarmasin in 2017. Collected blood was used for microscopic examination, sequencing using BLAST method to identify the nucleotide structure of cytochrome b (cyt b) gene that determines the species, and the phylogenetics analysis of L. caulleryi that infected broiler chickens in endemic areas in Indonesia, using Mega 5 software. Results: The results showed that Plasmodium sp. and L. caulleryi were infected broiler chickens in endemic areas in Indonesia. L. caulleryi in one area had very close phylogenetic relations with those in other areas. The genetic distance between L. caulleryi taxa from various endemic areas is very close (<5%). Conclusion: There is a very close phylogenetics among strains of L. caulleryi that infected broiler chickens in various endemic areas in Indonesia.
Scarperation: An Empirical Inquiry into the Role of Scarcity in Fostering Cooperation Between International River Riparians

The environment and security literature has argued that freshwater scarcity often leads to inter-state conflict, and possibly acute violence. The contention, however, ignores the long history of hydro-political cooperation exemplified by hundreds of documented agreements. Building on a theory that considers the relationship between scarcity and hydro-political cooperation, this paper empirically investigates why treaties are negotiated for some rivers and between some riparians, and not others. The paper suggests that long-term water scarcity has a significant influence on levels of cooperation. Additional variables considered include trade, level of governance among the riparian states, and the geography of the river. Findings confirm that cooperation and scarcity embody a concave (inverted U curve) relationship. Governance has a positive impact on cooperation. In addition, riparians may either arrange the use of their scarce water resources via a treaty or trade (and indirectly exchange [virtual]water). Scarcity, governance, and trade were found to be most salient in explaining levels of cooperation while geography is significant in some of the estimates.
Locally Checkable Labeling Problems in Rooted Trees in the Online-LOCAL Model of Computation

There are many ways to classify algorithms. Online algorithms, for example, are algorithms that have to be able to handle input one element at a time. Offline algorithms, on the other hand, have access to the whole input. In the case of online graph algorithms, the structure of the underlying graph is fixed. The graph is revealed to the algorithm one node at a time. When a node is revealed, the algorithm has to decide its output for that node, and it cannot change its decision later. Another way to classify algorithms is to divide them into centralized and distributed algorithms. In the case of graph algorithms, a centralized algorithm is a completely separate entity from the graph. When the nodes (or edges) of the graph are active parties in the execution of the algorithm, the algorithm is called a distributed algorithm. One commonly used model of distributed computation is the LOCAL model. In the LOCAL model, all nodes are computing their own part of the result in parallel. The nodes only see their own local neighborhood and need to base their decision only on this local view. In this thesis, I introduce the online-LOCAL model, which combines the power of online graph algorithms and LOCAL algorithms. Like online graph algorithms, online-LOCAL algorithms need to react to nodes being revealed one at a time. Unlike online graph algorithms, online-LOCAL algorithms also get to see the local neighborhood around the nodes before needing to make their decisions. The online-LOCAL model is a very strong model of computation. In general, there are problems that are trivial in the online-LOCAL model, but difficult to solve with online graph algorithms and LOCAL algorithms. In this thesis, I restrict my attention to the class of problems known as locally checkable labeling problems. These are a broad class of problems for which a solution is valid if it looks valid in all local neighborhoods. In particular, I show that for locally checkable labeling problems in rooted regular trees, the online-LOCAL model is approximately as powerful as the LOCAL model.
Combined obliquity and precession pacing of the late Pleistocene glacial cycles

Milankovitch postulated that deglaciation occurs when Earth’s obliquity is high and precession brings Earth’s eccentric orbit near the sun during Northern summer, and this general concept has been elaborated to show how precession, obliquity, or a combination of both could govern the timing of glaciation. Observational tests have demonstrated that obliquity paces the 100 ky glacial cycles but have been inconclusive with regard to precession, primarily because precession’s shorter period demands greater age accuracy. Here both obliquity (p<0.001) and precession (p=0.05) are shown to pace late Pleistocene glacial cycles. Requisite age control to test for precession pacing comes from tuning a composite 18 O record to align with obliquity. Likewise, precession is exclusively tuned to when testing for obliquity pacing, and the orthogonality between obliquity and precession guards against circularity in this process. The Milankovitch hypothesis is fully consistent with the test results, but not all other hypotheses are ruled out. In particular, the orbital configuration that maximizes insolation intensity at high northern latitudes also maximizes the duration of southern summers, and the latter may assist deglaciation through increasing the evasion of CO2 from the Southern Ocean into the atmosphere.
Kernel-machine-based classification in multi-polarimetric SAR data

The focus of this paper is the classification of military vehicles in multi-polarimetric high-resolution spotlight SAR images in an ATR framework. Kernel machines as robust classification methods are the basis of our approach. A novel kernel machine the Relevance Vector Machine with integrated Generator (RVMG) controlling the trade-off between classification quality and computational effort is used. It combines the high classification quality of the Support Vector Machine by margin maximization and the low effort of the Relevance Vector Machine caused by the special statistical approach. Moreover multi-class classification capability is given by an efficient decision heuristic, an adaptive feature extraction based on Fourier coefficients allows the module to do real time execution, and a parameterized reject criterion is proposed in this paper. Investigations with a nine class data set from QinetiQ deal with fully polarimetric SAR data. The objective is to assess polarimetric features in combination with several kernel machines. Tests approve the high potential of RVMG. Moreover it is shown that polarimetric features can improve the classification quality for hard targets. Among these the simple energy based features prove more favorable than complex ones. Especially the two coplanar polarizations embody the essential information, but a better generalizability is caused by using all four channels. An important property of a classifier used in the ATR framework is the capability to reject objects not belonging to any of the trained classes. Therefore the QinetiQ data are divided into four training classes and five classes of confusion objects. The classification module with reject criterion is controlled by the reject parameter and the kernel parameter. Both parameters are varied to determine ROC curves related to different polarimetric features.
1 A microtubule RELION-based pipeline for cryo-EM image processing

Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of αand β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.
Gorillas in our midst: sustained inattentional blindness for dynamic events

With each eye fixation, we experience a richly detailed visual world. Yet recent work on visual integration and change direction reveals that we are surprisingly unaware of the details of our environment from one view to the next: we often do not detect large changes to objects and scenes (`change blindness'). Furthermore, without attention, we may not even perceive objects (`inattentional blindness'). Taken together, these findings suggest that we perceive and remember only those objects and details that receive focused attention. In this paper, we briefly review and discuss evidence for these cognitive forms of `blindness'. We then present a new study that builds on classic studies of divided visual attention to examine inattentional blindness for complex objects and events in dynamic scenes. Our results suggest that the likelihood of noticing an unexpected object depends on the similarity of that object to other objects in the display and on how difficult the priming monitoring task is. Interestingly, spatial proximity of the critical unattended object to attended locations does not appear to affect detection, suggesting that observers attend to objects and events, not spatial positions. We discuss the implications of these results for visual representations and awareness of our visual environment.