Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor

Abstract Bacteriophage exclusion (‘BREX’) systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.
An Interview with John Dewey on Science Education.

Sooner or later almost all physics teachers are forced by the evidence to conclude that students do not attain understanding of concepts by listening to lectures — no matter how lucid they may be. A more fruitful alternative, which many teachers have arrived at independently, actively involves the students, starting with their own experiences and guiding them from there, through observation and reasoning, towards knowledge with understanding. There is great value in tracing the history of this educational thread: it confirms that the ideas have deep roots and have stood the test of time; it provides clues to the troubling question of why,! if this approach is so good, it is still not widely practiced; and, more importantly, it allows new thinking to start from “the shoulders of giants” rather than at ground level. One of these giants is John Dewey.
Macrophage efferocytosis in health and disease

Creating cellular homeostasis within a defined tissue typically relates to the processes of apoptosis and efferocytosis. A great example here is cell debris that must be removed to prevent unwanted inflammatory responses and then reduce autoimmunity. In view of that, defective efferocytosis is often assumed to be responsible for the improper clearance of apoptotic cells (ACs). This predicament triggers off inflammation and even results in disease development. Any disruption of phagocytic receptors, molecules as bridging groups, or signaling routes can also inhibit macrophage efferocytosis and lead to the impaired clearance of the apoptotic body. In this line, macrophages as professional phagocytic cells take the lead in the efferocytosis process. As well, insufficiency in macrophage efferocytosis facilitates the spread of a wide variety of diseases, including neurodegenerative diseases, kidney problems, types of cancer, asthma, and the like. Establishing the functions of macrophages in this respect can be thus useful in the treatment of many diseases. Against this background, this review aimed to recapitulate the knowledge about the mechanisms related to macrophage polarization under physiological or pathological conditions, and shed light on its interaction with efferocytosis.
Search for neutrinoless double beta decay with CUORICINO and prospects for CUORE

CUORICINO is a cryogenic detector running in Gran Sasso National Laboratory, Italy, since 2003. With its 40.7 kg mass of TeO2 mass, in the form of an array of 62 crystals, it has proven the feasibil- ity of the CUORE experiment, whose aim is to be sensitive to the effective neutrino mass as low as a few tens of meV. It has moreover set the current lower limit on the lifetime of 130 Te for neutrinoless double beta decay: we report on the up-to-date CUORICINO results and discuss the prospects for CUORE.
A HYBRID PHASE-FIELD BASED LATTICE BOLTZMANN METHOD FOR CONTACT LINE DYNAMICS

A hybrid phase-field based lattice Boltzmann method (LBM) is proposed in this paper to simulate the contact line dynamics. The flow field is obtained through the lattice Boltzmann equation (LBE). Concurrently, the interface capturing is accomplished by directly solving Cahn-Hilliard equation, which is the governing equation of interface evolution. A symmetric spatial discretization scheme is adopted to enhance the stability. Compared with the conventional algorithms which solve two sets of LBEs, the present method has several advantages such as reduction of the number of variables in the solution process, decoupling the mobility with relaxation time and enabling a more direct manner to implement wetting boundary conditions. The proposed algorithm is first validated through recovering the analytical profile of a surface layer. It is then applied to simulate droplet spreading on surfaces with different wettability.
Comparative Cluster/Double Star observations of the high and low latitude dayside magnetopause

The launch of the Double Star mission has provided the opportunity to monitor events at distinct locations on the dayside magnetopause, in coordination with the quartet of Cluster spacecraft. We present results of two such coordinated studies. In the first, 6 April 2004, both Cluster and the Double Star TC-1 spacecraft were on outbound transits through the dawn-side magnetosphere. Cluster observed northward moving FTEs with +/- polarity, whereas TC-1 saw -/+ polarity FTEs. The strength, motion and occurrence of the FTE signatures changes somewhat according to changes in IMF clock angle. These observations are consistent with ongoing reconnection on the dayside magnetopause, resulting in a series of flux transfer events (FTEs) seen both at Cluster and TC-1. The observed polarity and motion of each FTE signature advocates the existence of an active reconnection region consistently located between the positions of Cluster and TC-1, lying north and south of the reconnection line, respectively. This scenario is supported by the application of a model, designed to track flux tube motion, to conditions appropriate for the prevailing interplanetary conditions. The results from the model confirm the observational evidence that the low-latitude FTE dynamics is sensitive to changes in convected upstream conditions. In particular, changing the interplanetary magnetic field (IMF) clock angle in the model predicts that TC-1 should miss the resulting FTEs more often than Cluster, as is observed. For the second conjunction, on the 4 Jan 2005, the Cluster and TC-1 spacecraft all exited the dusk-side magnetosphere almost simultaneously, with TC-1 lying almost equatorial and Cluster at northern latitudes at about 4 RE from TC-1. The spacecraft traverse the magnetopause during a strong reversal in the IMF from northward to southward and a number of magnetosheath FTE signatures are subsequently observed. One coordinated FTE, studied in detail by Pu et al, (this issue), carries and inflowing energetic electron population and shows a motion and orientation which is similar at all spacecraft and consistent with the predictions of the model for the flux tube dynamics, given a near sub-solar reconnection line. This event can be interpreted either as the passage of two parallel flux tubes arising from adjacent x-line positions, or as a crossing of a single flux tube at different positions.
Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression

ABSTRACT Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.
THE COMPARATIVE STUDY OF CANNY FILTER AND MORPHOLOGICAL OPERATOR IN FINGERPRINT RECOGNITION

Fingerprint verification is one of the most reliable personal identification methods and it plays an important role in commercial and forensic applications. Designing a recognition system that will increase the accuracy is required. This thesis proposed a fingerprint recognition system using canny filter and morphological operator through path analysis test case. Steps involved in the recognition system include; image acquisition, pre-processing, features extraction and matching. Fast fourier transform is used to enhance the quality of the images and the features extracted efficiently to determine the minutia points in fingerprints with morphological operation, and the distribution of grey level co-occurrence matrix (GLCM) with canny filter. The proposed morphological operation determined the bifurcation, termination of the ridges and valleys, and their corresponding angles, and Euclidean distance was used for matching. On the other hand, features such as energy, homogeneity, entropy and correlation were extracted after canny filter was applied and again, Euclidean distance was used for matching. The experimental results showed the accuracy of the proposed methods through path analysis cases, and their performances were compared for their success rate, false accepted rate and false rejected rate. The overall success of the system under morphological algorithm was 99.70% with 0.15% false accepted rate and 0.30% false rejection rate. On the other hand, the overall accuracy obtained for GLCM, canny filter was 99.85% success rate with 0.15% false accepted rate and 0.15% false rejection rate. From the obtained results, it can be concluded that GLCM-canny filter overcame the morphological operation in obtaining high accuracy.
Persistent Neuroadaptations in the Nucleus Accumbens Core Accompany Incubation of Methamphetamine Craving in Male and Female Rats

Abstract Relapse is a major problem in treating methamphetamine use disorder. “Incubation of craving” during abstinence is a rat model for persistence of vulnerability to craving and relapse. While methamphetamine incubation has previously been demonstrated in male and female rats, it has not been demonstrated after withdrawal periods greater than 51 d and most mechanistic work used males. Here, we address both gaps. First, although methamphetamine intake was higher in males during self-administration training (6 h/d × 10 d), incubation was similar in males and females, with “incubated” craving persisting through withdrawal day (WD)100. Second, using whole-cell patch-clamp recordings in medium spiny neurons (MSNs) of the nucleus accumbens (NAc) core, we assessed synaptic levels of calcium-permeable AMPA receptors (CP-AMPARs), as their elevation is required for expression of incubation in males. In both sexes, compared with saline-self-administering controls, CP-AMPAR levels were significantly higher in methamphetamine rats across withdrawal, although this was less pronounced in WD100–135 rats than WD15–35 or WD40–75 methamphetamine rats. We also examined membrane properties and NMDA receptor (NMDAR) transmission. In saline controls, MSNs from males exhibited lower excitability than females. This difference was eliminated after incubation because of increased excitability of MSNs from males. NMDAR transmission did not differ between sexes and was not altered after incubation. In conclusion, incubation persists for longer than previously described and equally persistent CP-AMPAR plasticity in NAc core occurs in both sexes. Thus, abstinence-related synaptic plasticity in NAc is similar in males and females although other methamphetamine-related behaviors and neuroadaptations show differences.
An optimization network for solving a set of simultaneous linear equations

A network for solving systems of simultaneous linear equations based on Hopfield's neural network model with continuous, real-valued outputs is described. The network is composed of highly interconnected simple neurons with a linear transfer function at each node. It is guaranteed to converge to a correct solution for all solvable systems of equations irrespective of the choice of the node transfer function; the use of complex nonlinearities at the nodes only affects the network convergence time. When a system which admits a solution is given as input, the network converges spontaneously and rapidly to a very accurate solution in all cases. When an unsolvable system is provided as input, the network outputs fail to converge and make the energy function close to zero even after a very large number of iterations. <<ETX>>
Older Adults Receiving Rehabilitation Services Are More Likely to Get Bathing and Toileting Equipment Installed.

IMPORTANCE Adaptive equipment, such as shower grab bars and modified toilet seating, is effective but underused in the United States. To change this, a better understanding of how equipment ends up being installed is needed. We hypothesized that rehabilitation services were a major mechanism. OBJECTIVE To examine the association between receipt of rehabilitation services and installation of adaptive equipment. DESIGN Observational cohort of the National Health and Aging Trends Study in 2015 and 2016. SETTING Community. PARTICIPANTS A total of 416 community-dwelling adults age 65 yr or older who needed bathing equipment and 454 who needed toileting equipment. OUTCOMES AND MEASURES Study outcomes were the installation of bathing or toileting equipment. The primary independent variable was the receipt of rehabilitation services between 2015 and 2016. RESULTS Among older adults who needed equipment in 2015, 34.3% had bathing equipment and 19.2% had toileting equipment installed by 2016. In multivariate logistic regression analyses, rehabilitation services were associated with installation of bathing (odds ratio [OR] = 5.07, 95% confidence interval [CI] [2.60, 9.89]) and toileting equipment (OR = 2.67, 95% CI [1.48, 4.84]). CONCLUSIONS AND RELEVANCE A minority of those in need have adaptive equipment installed within a year. In the current health care system, rehabilitation providers play a major role in equipment installation. What This Article Adds: Rehabilitation providers are involved in the installation of adaptive bathroom equipment among older persons who need it. Still, most in need of equipment do not have it after a year, suggesting that further work is needed to increase access to rehabilitation providers and develop other avenues for obtaining equipment.
Characteristics of a slotted parallel-plate waveguide filled with a truncated dielectric

A slotted parallel-plate waveguide filled inside with a material which is truncated is analyzed. An integral equation is formulated for the slot electric field, and it is solved by the moment method. Data are presented for the slot electric field, a special aperture admittance, scattering parameters, and a far-field pattern. The special aperture admittance is a useful quantity in microstrip antenna design and is presented for various truncation lengths of the interior dielectric.
Transcriptional regulation of spatiotemporal gene expression within the seminiferous epithelium: Mouse Acrv1 gene as a model

Precise spatiotemporal expression of cohorts of differentiation markers unique to spermatogonia, spermatocytes, and round spermatids punctuates spermatogenesis and ensures its completion. For example, genes coding for the synaptonemal complex or the acrosome or flagellum are expressed sequentially in a developmental stage‐ and germ cell‐specific manner. But the transcriptional mechanisms governing the spatiotemporal order of gene expression within the seminiferous epithelium are poorly understood. Using the round spermatid‐specific Acrv1 gene, which codes for the acrosomal protein SP‐10 as a model, we learned that (1) the proximal promoter itself contains all the necessary cis‐regulatory sequences, (2) an insulator prevents somatic cell expression of the testis‐specific gene, (3) RNA II polymerase is loaded on the Acrv1 promoter but paused in spermatocytes, thus ensuring precise transcriptional elongation in round spermatids, and that (4) a transcriptional repressor binding protein of 43 kilodaltons (TDP‐43) plays a role in maintaining the paused state in spermatocytes. Although the Acrv1 enhancer element has been narrowed down to 50 bp and its binding to a 47 kDa testis‐abundant nuclear protein shown, the identity of the putative transcription factor responsible for activation of round spermatid‐specific transcription remains elusive. Human male infertility is idiopathic with limited treatment options. Understanding transcriptional regulation of spermatogenesis has the potential to lead to future therapies for male infertility.
Trajectories of physical and relational aggression across early childhood: Relations with peer risk factors.

The goal of the current study was to examine trajectories of relational and physical aggression in early childhood and evaluate peer predictors of these trajectories (i.e., peer rejection, relational victimization, and physical victimization). The study spanned three-time points (T1 in the spring, T2 in the fall, and T3 in the spring) in early childhood (N = 300; 44.0% girls; Mage = 44.70 months, SD = 4.38; 3.0% African American/Black, 7.6% Asian/Asian American/Pacific Islander, 1.0% Hispanic/Latinx, 11.3% multiracial, 62.1% White, and 15.0% missing/unknown). Observations of peer victimization and teacher report of peer rejection were collected at T1, and teacher report of aggression was collected at all time points. Results from piecewise latent growth models demonstrated that both forms of aggression decreased from T1 to T2 as children entered a new classroom and increased from T2 to T3 as they remained in that classroom. The increase in physical aggression from T2 to T3 was only significant for boys. Peer rejection at T1 emerged as a predictor of both intercepts and slopes from T1 to T2, and physical victimization predicted the physical aggression intercept and physical aggression slope from T1 to T2. Children high on these peer risk variables had higher initial levels of aggression, followed by a greater decrease in aggression from T1 to T2. Results underscore the importance of studying incremental change in aggression in early childhood and suggest that children who experience negative peer treatment have greater fluctuations in aggression over time.
Antitumor therapy for breast cancer: Focus on tumor‐associated macrophages and nanosized drug delivery systems

In breast cancer (BC), tumor‐associated macrophages (TAMs) are an important component of the tumor microenvironment and are closely related to poor prognosis. A growing number of studies have focused on the role of TAMs in BC progression and therapeutic strategies targeting TAMs. As an emerging treatment, the application of nanosized drug delivery systems (NDDSs) in the treatment of BC by targeting TAMs has attracted much attention.
Origin of geosynchronous relativistic electron events

[1] We have investigated the characteristics of solar wind and magnetospheric conditions associated with the occurrence of geosynchronous relativistic electron events. Most of the geosynchronous relativistic events for April 1999 to December 2002 are found to occur during prolonged (a number of days) quiet intervals following the appearance of high-speed solar wind streams. In a typical relativistic event, the electron fluxes begin to increase by orders of magnitude when the solar wind density drops after reaching a sharp peak at the leading edge of a high-speed stream. The increased fluxes stay at a high level until the quiet solar wind conditions cease. In addition, enhanced ULF wave activity and substorm injections of 10s to 100s keV electrons are observed at the time of the large flux increases in the events. We found that geosynchronous relativistic events can be observed only when both the solar wind and magnetospheric wave/substorm injection conditions are favorable regardless of whether or not a magnetic storm takes place. These observations suggest the following scenario for the occurrence of a geosynchronous relativistic electron event: (1) Quiet solar wind conditions (i.e., no strong solar wind pressure and large southward turnings of IMF Bz) can lead to stable and more dipole-like magnetospheric configurations in which the geosynchronous orbit is located well inside the trapping boundary of the energetic electrons. (2) If a large population of MeV electrons is generated (by some acceleration process(es) involving enhanced ULF wave and substorm injections) in the inner magnetosphere, it can be trapped and effectively accumulated to a high intensity. (3) The high electron flux can persist for a number of days in the geosynchronous region as long as the solar wind conditions remain quiescent. The occurrence of a geosynchronous relativistic electron event requires not only the proper acceleration process and sufficient seed electrons but also no significant loss process that dominates over any acceleration/source.
The roles of ubiquitin–proteasome system and regulator of G protein signaling 4 in behavioral sensitization induced by a single morphine exposure

Opioid addiction is a major public health issue, yet its underlying mechanism is still unknown. The aim of this study was to explore the roles of ubiquitin–proteasome system (UPS) and regulator of G protein signaling 4 (RGS4) in morphine‐induced behavioral sensitization, a well‐recognized animal model of opioid addiction.
Molecular Evidence of Leptospira spp. in Isolated Fijian Bats

Abstract: Bats host several zoonotic pathogens. Island biogeography and epidemiologic theory predict small remote islands have lower infection diversity. Molecular studies of urine and feces from three species at 10 sites from three islands suggest multiple pathogenic Leptospira, but not coronavirus, paramyxovirus, or Histoplasma, circulate in isolated Pacific Fijian bat populations.