Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction to: Mechanisms of coexistence in a diverse Neotropical mammalian carnivore community

Mammalian carnivore diversity within the Reserva Natural del Bosque Mbaracayú in eastern Paraguay is represented by five families (Canidae, Mephitidae, Mustelidae, Procyonidae, and Felidae) and includes large-bodied, apex predators, several omnivores, and numerous mesocarnivores. The competitive exclusion principle argues that sustained spatial and temporal coexistence of two or more species with identical ecological requirements is unsustainable. The Reserve is a mosaic of habitats that has become isolated due to extensive deforestation of the surrounding Upper Paraná Atlantic Forest. Nevertheless, it is remarkable in that 16 mammalian carnivore species are documented as coexisting within the Reserve. We sought to determine the extent to which this diverse community is mitigating competition through the partitioning of available niche space by assessing dietary ecology of mammalian carnivores present, including diet breadths and dietary overlap, and by examining spatial patterns within the reserve. Feces were collected from all 16 mammalian carnivore species from seven areas within the reserve and specific identifications were confirmed by molecular analyses. Diet breadth, ˆ B , standardized diet breadth, ˆ B A , and Pianka’s Index for dietary overlap, ˆ O , were calculated. A Chi-square goodness-of-fit test was performed to test for randomness of samples associated with survey areas. Diet analyses indicated a spectrum from dietary generalists to specialists. Species segregated into six dietary guilds, defined as groups of species with ˆ O > 0.5. Four guilds included only one species each (Neotropical otter, crab-eating fox, jaguar, and puma). The low dietary overlap between jaguar and puma contrasts with studies conducted elsewhere. One guild consisted of four highly omnivorous species (maned wolf, Molina’s hog-nosed skunk, crab-eating raccoon, and South American coati). The sixth guild included eight species which mostly consumed small vertebrates, primarily mammals as well as birds and reptiles (bush dog, two mustelines, five small felids). The mustelines (tayra and lesser grison) had extremely high dietary overlap. Although they did not segregate spatially, they are known to occupy distinct niches in vertically stratified forests. The five small felids also showed extremely high dietary overlap. Three of them were found to segregate spatially within the Reserve and two did not, although one (jaguarundi) is known to segregate temporally, being more active diurnally. The exceptionally rich community of mammalian carnivore species at the Reserva Natural del Bosque Mbaracayú appeared to avoid unsustainable competition by a variety of mechanisms, some utilizing different food items, or, in the case of high dietary overlap, utilizing spatial or temporal resources differently.
Extending higher‐dimensional quasi‐cocycles

Let G be a group admitting a non‐elementary acylindrical action on a Gromov hyperbolic space (for example, a non‐elementary relatively hyperbolic group, or the mapping class group of a closed hyperbolic surface, or Out(Fn) for n⩾2 ). We prove that, in degree 3, the bounded cohomology of G with real coefficients is infinite‐dimensional. Our proof is based on an extension to higher degrees of a recent result by Hull and Osin. Namely, we prove that if H is a hyperbolically embedded subgroup of G and V is any R[G] ‐module, then any n ‐quasi‐cocycle on H with values in V may be extended to G . Also, we show that our extensions detect the geometry of the embedding of hyperbolically embedded subgroups in a suitable sense.
Near-Neutral Surface Layer Turbulence at the Boulder Atmospheric Observatory Tower: Evidence of Increasing Vertical Turbulence with Height

Abstract Wind and turbulence profiles were analyzed during breezy, near-neutral conditions at the Boulder Atmospheric Observatory tower to quantify the effects of an abrupt 20- to 30-m increase in terrain located 3–5 km west of the tower. Results indicate that regional roughness length z0 is greatest and local z0 is smallest in sectors downwind of a long, shallow bluff, suggesting that distant, more complex, upwind terrain enhances horizontal turbulence but has little effect on local wind speed profiles. Turbulence parameter profiles are nearly constant up to 200 m above ground level (AGL), and friction velocity u∗ is nearly constant up to 150–200 m for simple fetch with z0 equal to 4 cm and near-surface wind speed approximately equal to 7 m s−1 at 10 m AGL. Horizontal turbulence parameters, however, increase by 50% to nearly 100% at all tower levels downwind of the distant terrain bluff when compared with those with simple fetch. The effect of the bluff on vertical turbulence increases with height. Altho.
Noise as a Key Factor in Realizing a Creative Society

To achieve a creative society, it is important to maintain a diversity of values. However, due to automatic alignment of values, maintaining diverse values is a chal- lenge. We propose that the noise, i.e, the uncertainty in understanding others’ values, may play a key role in realizing a creative society by moderating values alignment. In addition, the potential effects of noise may be affected by the social perception bias at the societal level. To study the dynamics of values diversity resulting from peer interactions with noise and perception bias, we present a hybrid opinion dynamics model, in which values is represented as both continuous and discrete categories. We simulate online social network- ing with various levels of noise and perception bias. We found that the positive effects of noise are twofold: it helps to moderate the alignment process of values within a group and to improve the social inclusiveness of extremism views. We conclude that noise contributes to preventing social fragmentation and monolithiciza- tion, and therefore plays a key role in realizing a creative society.
ON THE STEADY-STATE THERMOELASTIC PROBLEM FOR THE HALF-SPACE

This paper deals with the determination of the steady-state thermal stresses and displacements in a semi-infinite elastic medium which is bounded by a plane. The problem is treated within the classical theory of elasticity and is approached by the method of Green. It is shown that the stress field induced by an arbitrary distribution of surface temperatures is plane and parallel to the boundary. If the surface temperature is prescribed arbitrarily over a bounded "region of exposure" and is otherwise constant, the problem reduces to the determination of Boussinesq's three-dimensional logarithmic potential for a disk in the shape of the region of exposure, whose mass density is equal to the given temperature. Moreover, it is found that there exists a useful connection between the solutions to Boussinesq's and to the present problem for the half-space. An exact closed solution, in terms of complete and incomplete elliptic integrals of the first and second kind, is given for a circular region of exposure at uniform temperature. Exact solutions in terms of elementary functions are presented for a hemispherical distribution of temperature over a circular region, as well as for a rectangle at constant temperature. Introduction. Recent years have seen a revival of interest in the thermoelastic problem which has received repeated previous attention in the theory of elasticity.1 Nevertheless, the existing literature on this subject is largely confined to two-dimensional problems and to problems characterized by polar or rotational symmetry. A significant advance in connection with the general three-dimensional thermoelastic problem was made by Goodier [4], who considered a medium occupying the entire space; he reduced the computation of the thermal stresses due to an arbitrarily prescribed temperature distribution to the determination of the Newtonian potential for a mass distribution whose density coincides with the given temperature field. For domains other than the entire space, Goodier's approach merely supplies a particular solution of the thermoelastic equations and still necessitates the solution of an ordinary boundary-value problem in the theory of elasticity. A particular integral of the same form was employed earlier by Borchardt [5] in dealing with the special problem of the sphere. Goodier's method was extended by Mindlin and Cheng [6] to the problem of the half-space with a traction-free boundary, subjected to an arbitrary temperature distribution in its interior. As an application of the extended scheme, the problem of the half-space with a uniformly heated (or cooled) spherical core is solved in [6]. In the present paper we return to the problem of the half-space but limit our attention
Topological order in the fractional quantum Hall states

This thesis is focused on the theoretical characterization of topological order in non-Abelian fractional quantum Hall (FQH) states. The first part of the thesis is concerned with the ideal wave function approach to FQH states, where the idea is to try to obtain model wave functions and model Hamiltonians for all possible FQH states and to have a physical way of characterizing their topological order. I will explain recent attempts to do this through the so-called pattern of zeros framework and its relation to conformal field theory. The first chapter about the pattern of zeros introduces the basic concepts for single-component FQH states, how it relates to the conformal field theory approach to FQH wave functions, and how it can be used to derive various topological properties of FQH states. The second chapter extends the pattern of zeros framework to multi-component non-Abelian FQH states; this is an attempt at a full classification of possible topological orders in FQH states. Aside from the ideal wave function methods. the other known general method of constructing non-Abelian FQH states is through the parton construction. Here the idea is to break apart the electron into other fermions, called partons. and assume that they form integer quantum Hall states. This method allows us to describe all known FQH states. After reviewing the parton construction, I will demonstrate how it can be used to derive the low energy effective field theories for some of the most well-known non-Abelian FQH states, the Zk parafermion (Laughlin/Moore-Read/Read-Rezayi) states. The parton construction will motivate yet another topological field theory, the U(1) x U(1) x Z 2 Chern-Simons (CS) theory. I will demonstrate how to calculate many highly non-trivial topological properties of the U(1) x U(1) x Z 2 CS theory, such as ground state degeneracy on genus g surfaces and various fusion properties of the quasiparticles. Using the U(1) x U(1) x Z 2 CS theory, we will study phase transitions between bilayer Abelian states and non-Abelian states. The non-Abelian ones contain a series of new states, which we call the orbifold FQH states. These orbifold FQH states turn out to be important for the conceptual foundations of the pattern of zeros/vertex algebra approach to ideal FQH wave functions. We also find a series of non-Abelian topological phases which are not FQH states and do not have protected gapless edge modes that are separated from the deconfined phase of ZN gauge theories by a continuous phase transition. We give a preliminary analysis of these Z 2 "twisted" ZN topological phases. Thesis Supervisor: Xiao-Gang Wen Title: Cecil and Ida Green Professor of Physics
Fake it to break it: mimicking superinfection exclusion disrupts alphavirus infection and transmission in the yellow fever mosquito Aedes aegypti

Multiple viruses cause a phenomenon termed superinfection exclusion whereby a currently infected cell is resistant to secondary infection by the same or a closely related virus. In alphaviruses, this process is thought to be mediated, at least in part, by the viral protease (nsP2) which is responsible for processing the non-structural polyproteins (P123 and P1234) into individual proteins (nsP1-nsP4), forming the viral replication complex. Taking a synthetic-biology approach, we mimicked this naturally occurring phenomenon by generating a superinfection exclusion-like state in Aedes aegypti mosquitoes, rendering them refractory to alphavirus infection. By artificially expressing Sindbis virus (SINV) and chikungunya virus (CHIKV) nsP2 in mosquito cells and transgenic mosquitoes, we demonstrated a reduction in both SINV and CHIKV viral replication rates in cells following viral infection as well as reduced infection prevalence, viral titres and transmission potential in mosquitoes.
Relay Broadcast Channels with Confidential Messages

We investigate the effects of an additional relay node on the secrecy of broadcast channels by considering the model of relay broadcast channels with confidential messages. We show that this additional relay node can increase the achievable secrecy rate region of the broadcast channels with confidential messages. More specifically, first, we investigate the discrete memoryless relay broadcast channels with two confidential messages and one common message. Three inner bounds (with respect to decode-forward, generalized noise-forward and compress-forward strategies) and an outer bound on the capacity-equivocation region are provided. Second, we investigate the discrete memoryless relay broadcast channels with two confidential messages. Inner and outer bounds on the capacity-equivocation region are provided. Finally, we investigate the discrete memoryless relay broadcast channels with one confidential message and one common message. Inner and outer bounds on the capacity-equivocation region are provided, and the results are further explained via a Gaussian example. Compared with Csiszar-Korner's work on broadcast channels with confidential messages (BCC), we find that with the help of the relay node, the secrecy capacity region of the Gaussian BCC is enhanced.
Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence

All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins. These interactions are critical for mitochondrial function and eukaryotic fitness, and coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within taxa. Hybridization can disrupt coevolved interactions, resulting in hybrid breakdown, and mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Recently, signatures of strong selection to maintain compatible mitonuclear genotypes in hybrids have been detected in at least some inter-population crosses. However, this work has only been conducted in crosses between populations with extremely high levels of genetic divergence in both their mitochondrial and nuclear genomes, leaving the generality of strong selection for mitonuclear compatibility unclear. Here we address this limitation with reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. Our results show that the dominance of mitonuclear effects consistent with coevolved mitonuclear genotypes in fast-developing (i.e., high-fitness) hybrids is reduced in low-divergence crosses, but that selection to maintain mitonuclear compatibility is still observed on some nuclear chromosomes. Consequently, we demonstrate that, even at low levels of genetic divergence between taxa, mitonuclear incompatibilities may play a key role in the early stages of reproductive isolation.
CysPresso: Prediction of cysteine-dense peptide expression in mammalian cells using deep learning protein representations

Purpose: While many cysteine-rich peptides (CDPs) have potential therapeutic uses, our ability to identify CDPs that will express recombinantly in mammalian cells without prior experimentation is limited. To address this, we developed a novel machine learning model to predict the recombinant expressibility of CDPs based on primary sequence. Methods & Results: Random forest classifiers were trained using various protein representations based on natural language processing models (SeqVec), protein function (proteInfer), and protein structure (AlphaFold2). We found that all of these protein representations were useful at predicting CDP expressibility, though AlphaFold2 representations provided superior model performance. As AlphaFold2 generates multiple representations per peptide, we then sought to optimize the model by comparing its predictive success after training with different AlphaFold2 representation types. We found that concatenating the representations to create a combined AlphaFold2 representation yielded the best performance. To further improve model performance, we partitioned the model between knottins and non-knottins, which improved prediction of expressibility for knottins. Implementation of time-series classification further boosted performance of knottin expressibility prediction. Conclusion: We demonstrate that AlphaFold2 representations are suitable for tasks in addition to structure prediction, such as prediction of recombinant expressibility.
Monkey Dorsolateral Prefrontal Cortex Represents Abstract Visual Sequences during a No-Report Task

Monitoring sequential information is an essential component of our daily lives. Many of these sequences are abstract, in that they do not depend on the individual stimuli, but do depend on an ordered set of rules (e.g., chop then stir when cooking). Despite the ubiquity and utility of abstract sequential monitoring, little is known about its neural mechanisms. Human rostrolateral prefrontal cortex (RLPFC) exhibits specific increases in neural activity (i.e., “ramping”) during abstract sequences. Monkey dorsolateral prefrontal cortex (DLPFC) has been shown to represent sequential information in motor (not abstract) sequence tasks, and contains a subregion, area 46, with homologous functional connectivity to human RLPFC. To test the prediction that area 46 may represent abstract sequence information, and do so with parallel dynamics to those found in humans, we conducted functional magnetic resonance imaging (fMRI) in three male monkeys. When monkeys performed no-report abstract sequence viewing, we found that left and right area 46 responded to abstract sequential changes. Interestingly, responses to rule and number changes overlapped in right area 46 and left area 46 exhibited responses to abstract sequence rules with changes in ramping activation, similar to that observed in humans. Together, these results indicate that monkey DLPFC monitors abstract visual sequential information, potentially with a preference for different dynamics in the two hemispheres. More generally, these results show that abstract sequences are represented in functionally homologous regions across monkeys and humans. SIGNIFICANCE STATEMENT Daily, we complete sequences that are “abstract” because they depend on an ordered set of rules (e.g., chop then stir when cooking) rather than the identity of individual items. Little is known about how the brain tracks, or monitors, this abstract sequential information. Based on previous human work showing abstract sequence related dynamics in an analogous area, we tested whether monkey dorsolateral prefrontal cortex (DLPFC), specifically area 46, represents abstract sequential information using awake monkey functional magnetic resonance imaging (fMRI). We found that area 46 responded to abstract sequence changes, with a preference for more general responses on the right and dynamics similar to humans on the left. These results suggest that abstract sequences are represented in functionally homologous regions across monkeys and humans.
Rad51 inhibition sensitizes non-replicating quiescent cells to UVB radiation and transcription stress

DNA damage induced by environmental, occupational, and chemotherapeutic compounds lead to a variety of cellular responses that are potentially impacted by the proliferation status of the cell. Using small molecule inhibitors of various DNA doublestrand break (DSB) repair pathways in non-replicating, quiescent human cells exposed to UVB radiation, we unexpectedly observed a major role for the recombination protein Rad51 in promoting cell survival. In contrast to a previous report indicating a requirement for nucleotide excision repair (NER) in DSB formation after UV exposure in quiescent cells, we observed DSB formation and Rad51 function to be independent of NER. Moreover, our analyses of DNA damage response kinase signaling in quiescent cells identified protein substrates that were either dependent or independent of both NER and apoptotic signaling. Finally, we observed that Rad51 inhibition sensitized nonreplicating quiescent cells to diverse genotoxic stressors, including those inducing DNA- RNA hybrids and inhibiting transcription. Thus, these findings clarify the mechanisms by which DSBs arise in non-replicating cells and highlight the important role of Rad51 in promoting quiescent cell survival in response to general genotoxic stress. Summary statement DNA double strand breaks are generated independent of nucleotide excision repair in UV-irradiated quiescent cells and require the recombination protein Rad51 to promote cell survival.
Effects of nitrous oxide and ketamine on the prefrontal cortex in mice: a comparative study

Nitrous oxide (N2O; laughing gas) has recently been reported as a putative rapid-acting antidepressant, but little is known about the underlying mechanisms. We performed transcriptomics, in situ hybridization, and electrophysiological studies to examine the potential shared signatures induced by 1 h inhalation of 50% N2O and a single subanesthetic dose of ketamine in the medial prefrontal cortex (mPFC) in adult mice. Both treatments similarly affected the transcription of several negative regulators of mitogen-activated protein kinases (MAPKs), namely, dual specificity phosphatases. The effects were primarily located in the pyramidal cells. Notably, the overall effects of N2O on mRNA expression were much more prominent and widespread compared to ketamine. Ketamine caused an elevation of the spiking frequency of putative pyramidal neurons and increased gamma activity (30–100 Hz) of cortical local field potentials. However, N2O produced no such effects. Spiking amplitudes and spike-to-local field potential phase locking of putative pyramidal neurons and interneurons in this brain area showed no uniform changes across treatments. Thus, this study characterized the electrophysiological and transcriptome-wide changes in mPFC triggered by exposure to N2O and compared them with those caused by the rapid-acting antidepressant ketamine in terms of both the direction of their regulation and localization.