Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta

Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large “pores” in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1–4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.
Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity

The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered “Variants of Concern” by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
Summer decapod crustacean larval communities along the eastern Spanish Mediterranean coast

Decapod crustaceans are a diverse group englobing several species of commercial and ecological interest. In the Mediterranean Sea, decapod crustacean fisheries are among the most profitable, although in many cases their early life stages are poorly known. In this study, we tackle the composition and diversity patterns of the decapod larval communities along the eastern Spanish Mediterranean coast. Zooplankton sampling was carried out in surface waters at 101 stations from July 20th to August 31st 2016, over bottom depths between 90 and 1840 m. All shrimp larvae were identified to the lowest possible taxonomical level, and larvae from Anomura, Achelata and Brachyura were left at infraorder level. No larvae of Astacidea or Polychelida were found. The total zooplankton volume was estimated. A total of 20,022 decapod crustacean larvae were identified, focusing on shrimp taxa (suborder Dendrobranchiata and infraorder Caridea). Both zooplankton volume and decapod larval density values were higher in the northern part of the studied area, cut by deep submarine canyons. After assessing the diversity parameters of the decapod larval community, we present the summer mesoscale larval distribution of several species of commercial interest such as the caramote prawn (Penaeus kerathurus) or the deep-water rose shrimp (Parapenaeus longirostris). The northern submarine canyons are dominated by the presence of Penaeoidea, being the deep-sea shrimp Aristeus antennatus the dominant species in the community in this area, while the Sergestoidea are more abundant in the southern zone. This is the largest-scale study on decapod larvae mesoscale distribution in the Mediterranean Sea.
Collisional dissipation of Alfv\'{e}n waves in a partially ionised solar chromosphere

Certain regions of the solar atmosphere are at su ﬃ ciently low temperatures to be only partially ionised. The lower chromosphere contains neutral atoms, the existence of which greatly increases the e ﬃ ciency of the damping of waves due to collisional friction momentum transfer. More speciﬁcally the Cowling conductivity can be up to 12 orders of magnitude smaller than the Spitzer value, so that the main damping mechanism in this region is due to the collisions between neutrals and positive ions ([Khodachenko et al. 2004]). Using values for the gas density and temperature as functions of height taken from the VAL C model of the quiet Sun ([Vernazza et al 1981]), an estimate is made for the dependance of the Cowling conductivity on height and strength of magnetic ﬁeld. Using both analytic and numerical approaches the passage of Alfv´en waves over a wide spectrum through this partially ionised region is investigated. Estimates of the ef-ﬁciency of this region in the damping of Alfv´en waves are made and compared for both approaches. We ﬁnd that Alfv´en waves with frequencies above 0.6 Hz are completely damped and frequencies below 0.01 Hz una ﬀ ected.
Supercontinuum generation in suspended core microstructured tellurite optical fibers

We present the fabrication of tellurite TeO2-ZnO-Na2O (TZN) microstructured optical fibers (MOFs) with a suspended core and the characterization of their optical properties. The fibers are designed to develop an infrared supercontinuum generation using a sub-nJ femtosecond pulsed laser at 1. 56μm. By pumping a 20 cm long fiber we generate a supercontinuum (SC) spanning over 800 nm in the 1-2 μm wavelength range. For a MOF with a core size of 2.2 μm the zero dispersion wavelength (ZDW) is at 1.45 μm. The effective area of TZN MOF is 3.5 μm2 and the nonlinear coefficient is calculated to be 437 W-1km-1.
GPR183 antagonism reduces macrophage infiltration in influenza and SARS-CoV-2 infection

Rationale Severe viral respiratory infections are often characterised by extensive myeloid cell infiltration and activation and persistent lung tissue injury. However, the immunological mechanisms driving excessive inflammation in the lung remain poorly understood. Objectives To identify the mechanisms that drive immune cell recruitment in the lung during viral respiratory infections and identify novel drug targets to reduce inflammation and disease severity. Methods Preclinical murine models of influenza A virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Results Oxidised cholesterols and the oxysterol-sensing receptor GPR183 were identified as drivers of monocyte/macrophage infiltration to the lung during influenza A virus (IAV) and SARS-CoV-2 infection. Both IAV and SARS-CoV-2 infection upregulated the enzymes cholesterol 25-hydroxylase (CH25H) and cytochrome P450 family 7 subfamily member B1 (CYP7B1) in the lung, resulting in local production of the oxidised cholesterols 25-hydroxycholesterol (25-OHC) and 7α,25-dihydroxycholesterol (7α,25-OHC). Loss-of-function mutation of Gpr183 or treatment with a GPR183 antagonist reduced macrophage infiltration and inflammatory cytokine production in the lungs of IAV- or SARS-CoV-2-infected mice. The GPR183 antagonist significantly attenuated the severity of SARS-CoV-2 infection and viral loads. Analysis of single-cell RNA-sequencing data on bronchoalveolar lavage samples from healthy controls and COVID-19 patients with moderate and severe disease revealed that CH25H, CYP7B1 and GPR183 are significantly upregulated in macrophages during COVID-19. Conclusion This study demonstrates that oxysterols drive inflammation in the lung via GPR183 and provides the first preclinical evidence for the therapeutic benefit of targeting GPR183 during severe viral respiratory infections. Viral infections trigger oxysterol production in the lung, attracting macrophages via GPR183. Antagonising GPR183 reduced inflammation and disease severity in SARS-CoV-2 infection, making GPR183 a putative target for therapeutic intervention. https://bit.ly/3DXlJCY
The Risk Factors of Acute Coronary Syndrome in Young Women: A Systematic Review and Meta-Analysis

Background Acute coronary syndrome (ACS) has been one of the leading causes of mortality in the world. Despite common understanding regarding ACS as an older population’s or man's disease, the number of young women affected by this condition is increasing. Many studies have assessed the risk factors of ACS, but only a few studies focused on this subpopulation. Therefore, this systematic review and meta-analysis aim to evaluate the risk factors predisposing to ACS in the young women population. Methods Nine online databases were screened from the date of inception to September 2021, where the acquired studies were evaluated using the PRISMA statement. The inclusion criteria were a case control study with women age cut-off of <50 years. The risk factors of acute coronary syndrome were analyzed using a random-effect model, expressed as summary statistics of odds ratio (OR) for categorical variable and standard mean difference (SMD) for continuous data with normal distribution, with 95% confidence interval (CI). Quality assessment was conducted using the STROBE statement. Results Seven studies with the total of 7042 patients met the inclusion criteria of this meta-analysis. Diabetes mellitus, high BMI, obesity, hypercholestrolemia, hypertension, smoking, and family history significantly increased acute coronary syndrome risk in young women. Other risks such as heavy alcohol consumption, oral contraceptive use, and postmenopausal state were associated with higher risk of ACS. Conclusion The independent risk factors which are strongly related to ACS in young women were diabetes mellitus, hypertension, and hypercholesterolemia with odd ratios of 6.21, 5.32, and 4.07. Other risk factors which may be associated with an increased risk of ACS in young women were heavy alcohol consumption, oral contraceptive use, and postmenopausal state. Health promotion and effective intervention on this specific population regarding these risk factors can decrease young female cardiovascular morbidity and mortality as well as improved quality of life of women.
Band-gap and strain engineering in GeSn alloys using post-growth pulsed laser melting

The pseudomorphic growth of Ge1−x Sn x on Ge causes in-plane compressive strain, which degrades the superior properties of the Ge1−x Sn x alloys. Therefore, efficient strain engineering is required. In this article, we present strain and band-gap engineering in Ge1−x Sn x alloys grown on Ge a virtual substrate using post-growth nanosecond pulsed laser melting (PLM). Micro-Raman and x-ray diffraction (XRD) show that the initial in-plane compressive strain is removed. Moreover, for PLM energy densities higher than 0.5 J cm−2, the Ge0.89Sn0. 11 layer becomes tensile strained. Simultaneously, as revealed by Rutherford Backscattering spectrometry, cross-sectional transmission electron microscopy investigations and XRD the crystalline quality and Sn-distribution in PLM-treated Ge0.89Sn0. 11 layers are only slightly affected. Additionally, the change of the band structure after PLM is confirmed by low-temperature photoreflectance measurements. The presented results prove that post-growth ns-range PLM is an effective way for band-gap and strain engineering in highly-mismatched alloys.
Distance to Multidisciplinary Team Clinic in Gaborone, Botswana, and Stage at Cervical Cancer Presentation for Women Living With and Without HIV

PURPOSE Cervical cancer is the leading cause of cancer death for women in Botswana. Barriers in access to cancer care can lead to later stages at diagnosis and increased mortality. This study evaluated access, defined as travel time from a patient's residential village to a multidisciplinary team clinic in Gaborone, with stage of cervical cancer at presentation. In addition, because of the high HIV prevalence in Botswana, we explored the association between travel time and HIV status. METHODS Eligible patients with cervical cancer presenting to the multidisciplinary team between 2015 and 2020 were included. Data were abstracted from questionnaires and hospital records. Google Maps was used to calculate travel time. Multinomial regression was used to examine travel time and cancer stage, and multivariable logistic regression was used to investigate travel time and HIV status. RESULTS We identified 959 patients with cervical cancer of which 70.1% were women living with HIV. The median travel time was approximately 2 hours. Using a reference group of stage I disease and a travel time of < 1 hour, the odds of presenting with stage II increased for patients traveling 3-5 hours (adjusted odds ratio [OR], 2.00; 95% CI, 1.14 to 3.52) and > 5 hours (OR, 2.19; 95% CI, 1.15 to 4.19). There were no significant associations for stage III. For stage IV disease, the odds were increased for patients traveling 3-5 hours (OR, 2.93; 95% CI, 1.26 to 6.79) and > 5 hours (adjusted OR, 4.05; 95% CI, 1.62 to 10.10). In addition, the odds of patients presenting living with HIV increased with increasing travel time (trend test = 0.004). CONCLUSION This study identified two potential factors, travel time and HIV status, that influence access to comprehensive cervical cancer care in Botswana.
Primary Care Provider Demographics and Engagement in Interprofessional Collaboration

Introduction: Interprofessional care contributes to all components of the quadruple aim. While previous research has identified many facilitators and barriers to the provision of interprofessional care, whether demographic differences might influence the extent to which providers collaborate interprofessionally remains unknown. Methods: Using electronic health record data, we characterized the level of primary care providers’ (PCPs’) interprofessional collaboration based on the percent of their patients who had a visit with an interprofessional team member over a 14-month period. We then obtained demographic data, including gender, years in practice, and provider type, from the electronic health record and publicly available sources. Subsequently, we used linear regression to predict the PCPs’ level of interprofessional collaboration based on demographic indicators. Results: The median of each PCP’s patients who had a visit with an interprofessional team member during the study period was 12.6%. After controlling for the average age of the PCP’s patient panel, the PCP’s years in practice, and the PCP’s clinic, when compared with male PCPs, approximately 2% more of patients cared for by female PCPs had a visit with an interprofessional team member. Conclusion: Female providers are more likely to share their patients with an interprofessional team.
Big crunch avoidance in K=1 semiclassical loop quantum cosmology

It is well known that a closed universe with a minimally coupled massive scalar field always collapses to a singularity unless the initial conditions are extremely fine tuned. We show that the corrections to the equations of motion for the massive scalar field, given by loop quantum gravity in high curvature regime, always lead to a bounce independently of the initial conditions. In contrast to the previous works in loop quantum cosmology, we note that the singularity can be avoided even at the semi-classical level of effective dynamical equations with non-perturbative quantum gravity modifications, without using a discrete quantum evolution.
Coulomb drag between ballistic one-dimensional electron systems

The presence of pronounced electronic correlations in one-dimensional systems strongly enhances Coulomb coupling and is expected to result in distinctive features in the Coulomb drag between them that are absent in the drag between two-dimensional systems. In this review, we review recent Fermi and Luttinger liquid theories of Coulomb drag between ballistic one-dimensional electron systems, also known as quantum wires, in the absence of inter-wire tunnelling, to focus on these features and give a brief summary of the experimental work reported so far on one-dimensional drag. Both the Fermi liquid (FL) and the Luttinger liquid (LL) theory predict a maximum drag resistance RD when the one-dimensional subbands of the two quantum wires are aligned and the Fermi wave vector kF is small, and also an exponential decay of RD with increasing inter-wire separation, both features confirmed by experimental observations. A crucial difference between the two theoretical models emerges in the temperature dependence of the drag effect. Although the FL theory predicts a linear temperature dependence, the LL theory promises a rich and varied dependence on temperature depending on the relative magnitudes of the energy and length scales of the systems. At very low temperatures, the drag resistance may diverge due to the formation of locked charge density waves. At higher temperatures, it should show a power-law dependence on temperature, RD Tx, experimentally confirmed in a narrow temperature range, where x is determined by the Luttinger liquid parameters. The spin degree of freedom plays an important role in the LL theory in predicting the features of the drag effect and is crucial for the interpretation of experimental results. Substantial experimental and theoretical work remains to be done for a comprehensive understanding of one-dimensional Coulomb drag.
Synchondrosis fusion contributes to the progression of postnatal craniofacial dysmorphology in syndromic craniosynostosis

Syndromic craniosynostosis (CS) patients exhibit early, bony fusion of calvarial sutures and cranial synchondroses, resulting in craniofacial dysmorphology. In this study, we chronologically evaluated skull morphology change after abnormal fusion of the sutures and synchondroses in mouse models of syndromic CS for further understanding of the disease. We found fusion of the inter‐sphenoid synchondrosis (ISS) in Apert syndrome model mice (Fgfr2S252W/+) around 3 weeks old as seen in Crouzon syndrome model mice (Fgfr2cC342Y/+). We then examined ontogenic trajectories of CS mouse models after 3 weeks of age using geometric morphometrics analyses. Antero‐ventral growth of the face was affected in Fgfr2S252W/+ and Fgfr2cC342Y/+ mice, while Saethre–Chotzen syndrome model mice (Twist1+/−) did not show the ISS fusion and exhibited a similar growth pattern to that of control littermates. Further analysis revealed that the coronal suture synostosis in the CS mouse models induces only the brachycephalic phenotype as a shared morphological feature. Although previous studies suggest that the fusion of the facial sutures during neonatal period is associated with midface hypoplasia, the present study suggests that the progressive postnatal fusion of the cranial synchondrosis also contributes to craniofacial dysmorphology in mouse models of syndromic CS. These morphological trajectories increase our understanding of the progression of syndromic CS skull growth.
The causal role of affect sharing in driving vicarious fear learning

Vicarious learning, i.e. learning through observing others rather than through one’s own experiences, is an integral skill of social species. The aim of this study was to assess the causal role of affect sharing, an important aspect of empathy, in vicarious fear learning. N = 39 participants completed a vicarious Pavlovian fear conditioning paradigm. In the learning stage, they watched another person–the demonstrator–responding with distress when receiving electric shocks to a color cue (conditioned stimulus; CS+; a different color served as CS-). In the subsequent test stage, an increased skin conductance response (SCR) to the CS+ presented in the absence of the demonstrator indexed vicarious fear learning. Each participant completed this paradigm under two different hypnotic suggestions, which were administered to induce high or low affect sharing with the demonstrator in the learning stage, following a counterbalanced within-subject design. In the learning stage, high affect sharing resulted in stronger unconditioned SCR, increased eye gaze toward the demonstrator’s face, and higher self-reported unpleasantness while witnessing the demonstrator’s distress. In the test stage, participants showed a stronger conditioned fear response (SCR) when they had learned under high, compared to low, affect sharing. In contrast, participants’ declarative memory of how many shocks the demonstrator had received with each cue was not influenced by the affect sharing manipulation. These findings demonstrate that affect sharing is involved in enhancing vicarious fear learning, and thus advance our understanding of the role of empathy, and more generally emotion, in social observational learning.