Miracle-dz/UniFAR-FTUs huggingface dataset:
Superhydrophobic Rotation-Chip for Computer-Vision Identification of Drug-Resistant Bacteria

The transport, distribution, and mixing of microfluidics often require additional instruments, such as pumps and valves, which are not feasible when operated in point-of-care (POC) settings. Here, we present a simple microfluidic pathogen detection system known as Rotation-Chip that transfers the reagents between wells by manually rotating two concentric layers without using external instruments. The Rotation-Chip is fabricated by a simple computer numerical control (CNC) machining process and is capable of carrying out 60 multiplexed reactions with a simple 30-degree or 60-degree rotation. Leveraging superhydrophobic coating, a high fluid transport efficiency of 92.78% is achieved without observable leaking. Integrated with an intracellular fluorescent assay, an on-chip detection limit of 1.8×106 CFU/mL is achieved for ampicillin-resistant Escherichia coli (E. coli), which is similar to our off-chip results. We also develop a computer vision method to automatically distinguish positive and negative samples on the chip, showing 100% accuracy. Our Rotation-Chip is simple, low-cost, high-throughput, and can display test results with a single chip image, ideal for various multiplexing POC applications in resource-limited settings.
Assessment of changes in neural activity during acquisition of spatial knowledge using EEG signal classification

Objective. This study explored the classification of electroencephalography (EEG) signals to assess changes in neural activity as individuals performed a training task in a virtual environment simulator. Commonly, task behavior and perception are used to assess a trainee’s ability to perform a task, however, changes in cognition are not usually measured and could be important to provide a true indication of an individual’s level of knowledge or skill. Approach. In this study, 15 participants acquired spatial knowledge via 60 navigation trials (divided into ten blocks) in a novel virtual environment. Time performance, perceived certainty, and EEG signal data were collected. Main results. A significant increase in alpha power and classification accuracy of EEG data from block 1 against blocks 2–10 was observed and stabilized after block 7, while time performance and perceived certainty measures improved and stabilized after block 5 and 6, respectively. Significance. Results suggest that changes in neural activity, which may reflect an increase in cognitive efficiency, could provide additional insight beyond time performance and perceived certainty.
A multicolor suite for deciphering population coding in calcium and cAMP in vivo

cAMP is a pivotal second messenger regulated by various upstream pathways including Ca2+ and G protein-coupled receptors (GPCRs). To decipher in vivo cAMP dynamics, we rationally designed cAMPinG1, an ultrasensitive genetically encoded green cAMP indicator that outperformed its predecessors in both dynamic range and cAMP affinity. Two-photon cAMPinG1 imaging detected cAMP transients in the somata and dendritic spines of neurons in the mouse visual cortex on the order of tens of seconds. In addition, multicolor imaging with a highly sensitive new red Ca2+ indicator RCaMP3 allowed simultaneous measurement of population patterns in Ca2+ and cAMP in hundreds of neurons. We identified Ca2+-induced cAMP responses that represented specific information, such as direction selectivity in vision and locomotion, as well as GPCR-induced cAMP responses. Overall, our multicolor suite revealed that information encoded in Ca2+ and GPCRs signaling is integrated and stored as cAMP transients for longer periods in vivo. Highlights Developing an ultrasensitive cAMP indicator, cAMPinG1, for visualizing cAMP transients in somata and dendritic spines in vivo. Developing a highly sensitive red Ca2+ indicator, RCaMP3, for visualizing Ca2+ transients in large neuronal population. Dual-color Ca2+ and cAMP imaging for dissecting Ca2+-induced and GPCR-induced cAMP responses. Single-cell, single-timepoint cAMP imaging for GRCR biology and drug screening.
Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern

The high mutation rate of SARS-CoV-2 leads to emergence of several variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors – cell proteins required for viral replication - would help avoid resistance. However, whether different SARS-CoV-2 variants induce conserved cell responses and exploit the same core host factors is still unclear. We compared three variants of concern and observed that the host transcriptional response was conserved, differing only in kinetics and magnitude. By CRISPR screening we identified the host genes required for infection by each variant: most of the identified genes were shared by multiple variants, both in lung and colon cells. We validated our hits with small molecules and repurposed FDA-approved drugs. All drugs were highly effective against all tested variants, including delta and omicron, new variants that emerged during the study. Mechanistically, we identified ROS production as a pivotal step in early virus propagation. Antioxidant drugs, such as N-acetyl cysteine (NAC), were effective against all variants both in human lung cells, and in a humanised mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.
Temporal Dynamics of Activity in Default Mode Network Suggest a Role in Top-Down Processing for Trial Responses

The default mode network (DMN) is a collection of brain regions including midline frontal and parietal structures, medial and lateral temporal lobes, and lateral parietal cortex. Although there is evidence that the network can be subdivided into at least two subcomponents, the network reliably exhibits highly correlated activity both at rest and during task performance. Current understanding regarding the function of the DMN rests on a large body of research indicating that activity in the network decreases during task epochs of experimental paradigms relative to inter-trial intervals. A seeming contradiction arises when the experimental paradigm includes tasks involving autobiographical memory, thinking about one’s self, planning for the future, or social cognition. In such cases, the DMN’s activity increases and is correlated with attentional networks. Some have therefore concluded that the DMN supports advanced human cognitive abilities such as interoceptive processing and theory of mind. This conclusion may be called into question by evidence of correlated activity in homologous brain regions in other, even non-primate, species. Thus, there are contradictory findings related to the function of the DMN that have been difficult to integrate into a coherent theory regarding its function. Using data from the Human Connectome Project, we explore the temporal dynamics of activity in different regions of the DMN in relation to stimulus presentation. We show that generally the dorsal portion of the network exhibits only a transient initial decrease in activity at the start of trials that increases over trial duration. The ventral component often has more similarity in its time course to that of task-activated areas. We propose that task-associated ramping dynamics in the network are incompatible with a task-negative view of the DMN and propose the dorsal and ventral sub-components of network may rather work together to support bottom-up salience detection and subsequent top-down voluntary action. In this context, we re-interpret the body of anatomical and neurophysiological experimental evidence, arguing that this interpretation can accommodate the seeming contradictions regarding DMN function in the extant literature.
Macrophages only sense infectious SARS-CoV-2 when they express sufficient ACE2 to permit viral entry, where rapid cytokine responses then limit viral replication

Macrophages are key cellular contributors to COVID-19 pathogenesis. Whether SARS-CoV-2 can enter macrophages, replicate and release new viral progeny remains controversial. Similarly, whether macrophages need to sense replicating virus to drive cytokine release is also unclear. Macrophages are heterogeneous cells poised to respond to their local microenvironment, and accordingly, the SARS-CoV-2 entry receptor ACE2 is only present on a subset of macrophages at sites of human infection. Here, we use in vitro approaches to investigate how SARS-CoV-2 interacts with ACE2-negative and ACE2-positive human macrophages and determine how these macrophage populations sense and respond to SARS-CoV-2. We show that SARS-CoV-2 does not replicate within ACE2-negative human macrophages and does not induce pro-inflammatory cytokine expression. By contrast, ACE2 expression in human macrophages permits SARS-CoV-2 entry, replication, and virion release. ACE2-expressing macrophages sense replicating virus to trigger pro-inflammatory and anti-viral programs that limit virus release. These combined findings resolve several controversies regarding macrophage-SARS-CoV-2 interactions and identify a signaling circuit by which macrophages sense SARS-CoV-2 cell entry and respond by restricting viral replication. One sentence summary Lack of macrophage ACE2 expression precludes SARS-CoV-2 entry and sensing, while ACE2-expressing macrophages sense intramacrophage SARS-CoV-2 replication to induce rapid anti-viral responses that limit new virion release.
Modulation of functional networks related to the serotonin neurotransmitter system by citalopram: Evidence from a multimodal neuroimaging study

Background: Selective serotonin reuptake inhibitors (SSRIs) potentiate serotonergic neurotransmission by blocking the serotonin transporter (5-HTT), but the functional brain response to SSRIs involves neural circuits beyond regions with high 5-HTT expression. Currently, it is unclear whether and how changes in 5-HTT availability after SSRI administration modulate brain function of key serotoninergic circuits, including those characterized by high availability of the serotonin 1A receptor (5-HT1AR). Aim: We investigated the association between 5-HTT availability and 5-HTT- and 5-HT1AR-enriched functional connectivity (FC) after an acute citalopram challenge. Methods: We analyzed multimodal data from a dose–response, placebo-controlled, double-blind study, in which 45 healthy women were randomized into three groups receiving placebo, a low (4 mg), or high (16 mg) oral dose of citalopram. Receptor-Enhanced Analysis of functional Connectivity by Targets was used to estimate 5-HTT- and 5-HT1AR-enriched FC from resting-state and task-based fMRI. 5-HTT availability was determined using [123I]FP-CIT single-photon emission computerized tomography. Results: 5-HTT availability was negatively correlated with resting-state 5-HTT-enriched FC, and with task-dependent 5-HT1AR-enriched FC. Our exploratory analyses revealed lower 5-HT1AR-enriched FC in the low-dose group compared to the high-dose group at rest and the placebo group during the emotional face-matching task. Conclusions: Taken together, our findings provide evidence for differential links between 5-HTT availability and brain function within 5-HTT and 5-HT1AR pathways and in context- and dose-dependent manner. As such, they support a potential pivotal role of the 5-HT1AR in the effects of citalopram on the brain and add to its potential as a therapeutic avenue for mood and anxiety disturbances.
Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention

RNA-directed DNA methylation in plants is guided by 24 nt siRNAs generated in parallel with 23 nt RNAs of unknown function. We show that 23 nt RNAs function as passenger strands during 24 nt siRNA incorporation into AGO4. The 23 nt RNAs are then sliced into 11 and 12 nt fragments, with 12 nt fragments remaining associated with AGO4. Slicing recapitulated with recombinant AGO4 and synthetic RNAs reveals that siRNAs of 21-24 nt, with any 5’ terminal nucleotide, can guide slicing, with sliced RNAs then retained by AGO4. In vivo, RdDM target locus RNAs that copurify with AGO4 also display a sequence signature of slicing. Comparing plants expressing slicing-competent versus slicing-defective AGO4 shows that slicing elevates cytosine methylation levels at virtually all RdDM loci. We propose that siRNA passenger strand elimination and AGO4 tethering to sliced target RNAs are distinct modes by which AGO4 slicing enhances RNA-directed DNA methylation.
Recent Response of Vegetation Water Use Efficiency to Climate Change in Central Asia

Quantifying the coupled cycles of carbon and water is essential for exploring the response mechanisms of arid zone terrestrial ecosystems and for formulating a sustainable and practical solution to issues caused by climate change. Water use efficiency (WUE), one of the comprehensive indicators for assessing plant growth suitability, can accurately reflect vegetation’s dynamic response to changing climate patterns. This study assesses the spatio-temporal changes in WUE (ecosystem water use efficiency, soil water use efficiency, and precipitation water use efficiency) from 2000 to 2018 and quantifies their relationship with meteorological elements (precipitation, temperature, drought) and the vegetation index (NDVI). The study finds that the sensitivity of NDVI to WUE is highly consistent with the spatial law of precipitation. The εPre threshold range of different types of WUE is about 200 mm or 1600 mm (low-value valley point) and 300 mm or 1500 mm (high-value peak point), and the εTem threshold value is 3~6 °C (high-value peak point) and 9~12 °C (low-value valley point). The degree to which vegetation WUE is influenced by precipitation is positively correlated with its time lag, whereas the degree to which temperature influences vegetation is negatively correlated. The WUE time lag is very long in hilly regions and is less impacted by drought; it is quite short in plains and deserts, where it is substantially affected by drought. These findings may be of great significance in responding to the severe situation of increasingly scarce water resources and the deterioration of the ecological environment across Central Asia.
Magnetic reconnection induced by weak Kelvin‐Helmholtz instability and the formation of the low‐latitude boundary layer

We have performed two‐dimensional two‐fluid simulations including finite electron inertial effects to investigate the role of Kelvin‐Helmholtz Instability (KHI) on the formation of Low‐Latitude Boundary Layer (LLBL). The results from a case in which the magnetic field components along the k‐vector of the KHI are anti‐parallel across the shear layer indicate that KHI forces magnetic reconnection as its flow compresses the current sheet in its early phase. Reconnection can be triggered even when the Alfven Mach number of the shear (MA) is small (2 < MA < 5: weak KHI). The reconnection process allows the vortex to highly roll‐up and thus to form a large scale mixing region. The results imply that the combination of anti‐parallel geometry and weak‐KHI may play an important role in the formation of the LLBL, which is obtained rather commonly for a realistic LLBL situation under northward IMF.
Estimating the prevalence of male clients of prostitute women in Vancouver with a simple capture–recapture method

Summary. Capture–recapture techniques are widely used to estimate the size of difficult‐to‐count human populations. Applications often focus on the overlap between two or more samples, but another type of data that is encountered in human studies involves only the number of times that particular individuals were encountered in the study period. We present a method for estimating the population size in this situation. This method is simple and technically accessible and allows for entries and exits by individuals and for a difference between probabilities of initial and subsequent contacts. We apply the method to arrest data on male clients of prostitute women in Vancouver.
Twist defect in an imprinted cholesteric elastomer

We have found that a chiral twist defect inserted in a cholesteric elastomer gives rise to circularly polarized localized modes of both handedness. This defect enhances the resonant mode amplitude whose handedness is opposite to that of the cholesteric helix for high cross-linked density, whereas for low cross-linked density, the same mode is decoupled with the defect and thus the resonant mode disappears. Finally, the resonant mode of the same handedness as the elastomer helix is maintained for both high and low cross-linked density.
Localization of real and virtual sound sources

Localization of real and virtual sound sources was studied using two tasks. In the first task, subjects had to turn their head while the sound was continuously on and press a button when they thought they faced the source. In the second task, the source only produced a short sound and the subjects had to indicate, by pressing one of eight buttons, in which quadrant the source was located, and whether it was located above or below the horizontal plane. Virtual sound sources were created using head‐related transfer functions (HRTFs), measured with probe microphones placed in the ear canals of the subjects. Sound stimuli were harmonic signals with a fundamental frequency of 250 Hz and an upper frequency ranging from 4 to 15 kHz. Results, obtained from eight subjects, show that localization performance for real and virtual sources was similar in both tasks, provided that the stimuli did not contain frequencies above 7 kHz. When frequencies up to 15 kHz were included, performance for virtual sources was, in ge.
A qualitative exploration of the lived experiences and perceived impact of a supportive-expressive group therapy on men living with gastrointestinal cancer

Supplemental Digital Content is Available in the Text. Abstract Background: This study seeks to understand the functioning of a gastrointestinal (GI) men-only Supportive-Expressive Group Therapy (SEGT) program over time by exploring (1) men's lived experiences with group process and (2) perceived group impact relevant to supportive/expressive goals. Methods: A convenience sample of patients with GI cancer attending an ongoing, men-only GI cancer SEGT was interviewed at 3 and 6 months from enrollment. A qualitative study design with mixed inductive and framework thematic analysis was used. Open-ended, semistructured interviews directed the exploration of group experiences over time. SEGT goals framed the inquiry toward exploring the perceived impact of the group. Results: Twenty-three men were interviewed at 3 months and 13 men at 6 months of intervention. Men pointed to an overall global satisfaction with group process and subjects discussed. The SEGT model provided a sex sensitive, safe, and mutually supportive outlet for expressing and normalizing participants' feelings and emotions. Three central themes emerged relevant to group experiences: (1) the role of social comparison, (2) the role of supportive-expressive exchanges, and (3) the role of the group format, composition, and facilitation. Feeling heard and validated accelerated a sense of belonging and facilitated emotional disclosure. SEGT contributed to re-evaluation of life values/goals, mitigation of existential anxiety, and mood improvement. Conclusions: Group participants perceived the SEGT as effective in addressing and mitigating emotional and existential concerns. Perceived benefits were consistent with SEGT goals. The findings offer groundwork for developing men-centered cancer support groups that foster emotional exploration and expressive disclosure through validation and acceptance.
Vortex ring formation at tube and orifice openings

The formation, at tube and orifice openings, of vortex rings generated by a piston moving with velocity proportional to time to some power m, is considered. The expansion of the axisymmetric generating flow about the circular forming edge is used in conjunction with the similarity theory of edge vortex growth to model the ring formation process. For large Reynolds numbers the ring diameter and circulation are not strongly dependent on the piston velocity profile. However, the ring viscous subcore shows peaks in the tangential velocity profile only if m < (π–θ)/(2π–θ), where θ is the edge forming angle.
Difference sets in Abelian groups

1. Difference sets in finite groups have been studied at great lengtll in a paper by R. H. Bruck [I]. Marshall Hall, Jr.'s notion of a "multiplier" of a difference set has been extended by Bruck to difference sets in groups. The latter has also extended a theorem of Hall on multipliers [3] to abelian groups. Hall has later obtained a generalization of his theorem. The object of this paper is, in the first instance, to extend this generalized theorem of Hall on multipliers to difference sets in abelian groups. A new feature that has been introduced here is the application of the theory of characters to the discussion of the problem. By this method I have also been able to obtain a new class of different sets. The later part of the paper is concerned with the discussion of this new class. Let G be an abelian group of order v and let D be a subset of G containing k elements such that every element of G other than the identity can be expressed exactly X times in the form ab-' where a, b are elements of D. Then D is called a difference set of type (v, k, X). The numbers v, k, X satisfy the relation
Vertex ordering and partitioning problems for random spatial graphs

Given an ordering of the vertices of a ﬁnite graph, let the induced weight for an edge be the separation of its endpoints in the ordering. Layout problems involve choosing the ordering to minimize a cost functional such as the sum or maximum of the edge weights. We give growth rates for the costs of some of these problems on supercritical percolation processes and supercritical random geometric graphs, obtained by placing vertices randomly in the unit cube and joining them whenever at most some threshold distance apart.
Solutions of Impulsive Diffusion and Von-Foerster-Makendrick Models Using the B-Transform

In this paper we explore the possibility of using the scientific computing method to obtain the inverse B-Transform of Oyelami and Ale [1]. Using some suitable conditions and the symbolic programming method in Maple 15 we obtained the asymptotic expansion for the inverse B-transform then used the residue theorem to obtain solutions of Impulsive Diffusion and Von-Foerster-Makendrick models. The results obtained suggest that drugs that are needed for prophylactic or chemotherapeutic purposing the concentration must not be allowed to oscillate about the steady state. Drugs that are to be used for immunization should not oscillate at steady state in order to have long residue effect in the blood. From Von-Foerster-Makendrick model, we obtained the conditions for population of the specie to attain super saturation level through the “dying effect” phenomenon ([2-4]). We used this phenomenon to establish that the environment cannot accommodate the population of the specie anymore which mean that a catastrophic stage t * is reached that only the fittest can survive beyond this regime (i.e. t > t * ) and that there would be sharp competition for food, shelter and