Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural classification of αββ and ββα supersecondary structure units in proteins

We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen‐bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well‐resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α–β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α–β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database‐derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193–212, 1998. © 1998 Wiley‐Liss, Inc.
Emerald Ash Borer in the Ash (Fraxinus spp.)-Dominated Tidal Swamps of the Lower Patuxent River, Maryland

Abstract - The tidal swamps of the near coastal rivers dominated by ash species (Fraxinus spp.) on the Mid-Atlantic coast of the United States are a globally rare and diverse habitat and, with the invasion of Agrilus planipennis (Emerald Ash Borer [EAB]), are under threat of alteration due to EAB-caused ash mortality. Little to no information exists on the effects that EAB infestation has had on these tidal swamps; therefore, the purpose of this study was to explore the current state of overstory health, regeneration, and herbaceous plant community at an ash-dominated tidal swamp on the lower Patuxent River, MD. It was found that, in comparison to adjacent stands of ash in the bottomland hardwood forest, the tidal swamp had a significantly larger proportion of its stand basal area infested or killed by EAB. On the other hand, the degree of regeneration of ash stems was far greater in the tidal swamp in terms of seedlings, basal shoots, and young trees. Finally, the herbaceous plant communities were determined to be distinct to their respective habitat types and would likely have different responses to the loss of ash. I concluded that the observed effects of EAB infestation were not the same between the habitat types and that the tidal swamp should be considered separately in management plans for EAB in the Mid-Atlantic and Chesapeake Bay regions.
Synthesis and characterization of nanocrystalline tungsten oxide nanosheets in large scale

A high quantity of tungsten oxide nanosheets were synthesized by oxidizing tungsten plates with potassium hydrate as the catalyst and tungsten plate as the substrate. The structural and geometrical properties were characterized by various techniques. It was found that the crystalline nanosheets have a WO_3 structure with thicknesses of 30–50 nm and widths up to tens of micrometers. There exist two characteristic acute angles of about 37° or 51° on the nanosheet plane. The formation of these angles and the growth mechanism were discussed.
Lime and Cattle Manure in Soil Fertility and Soybean Grain Yield Cultivated in Tropical Soil

Most tropical soils have high acidity and low natural fertility. The appropriate application of lime and cattle manure corrects acidity, improves physical and biological properties, increases soil fertility, and reduces the use of chemical and/or synthetic fertilizers by crops, such as soybean, the main agricultural export product of Brazil. This study aimed to assess the effects of the combination of the application of dolomite limestone (0, 5, and 10 Mg ha−1) and cattle manure (0, 40, and 80 Mg ha−1) on grain yield and the chemical properties of an Oxisol (Red Latosol) cultivated with soybean for two consecutive years. The maximum grain yield was obtained with the application of 10 Mg ha−1 of lime and 80 Mg ha−1 of cattle manure. Liming significantly increased pH index, the concentrations of calcium (Ca2+) and exchangeable magnesium (Mg2+), and cation exchange capacity (CEC) of soil and reduced potential acidity (H+ + Al3+), while the application of cattle manure increased pH level; the concentrations of potassium (K+), Ca2+, and exchangeable Mg2+; and CEC of the soil. During the 2 years of assessment, the greatest grain yields were obtained with saturation of K+, Ca2+, and Mg2+ in CEC at the 4.4, 40.4, and 17.5 levels, respectively. The results indicated that the ratios of soil exchangeable Ca/Mg, Ca/K, K/Mg, and K/(Ca+Mg) can be modified to increase the yield of soybean grains.
NOTES ON THE EFFECT OF NOISE ON LANGMUIR PROBE CHARACTERISTICS

A partial analysis has been made of the effects of fluctuations in a plasma on the data obtained by conventional use of Langmuir probes. Consideration has been given to effects of periodic fluctuations of electron temperature, random current and space-potential, supposed independent of probe potential. For a wide range of conditions, the values of electron temperature obtained will be correct, but values of electron concentration underestimated. Experiments are described to check part of the theory, and the bearing of the experimental and theoretical results obtained on the probe analysis of discharges in which there are plasma electron oscillations is discussed briefly.
Streptococcus pneumoniae Meningitis and Intracranial Vasculopathy: Clinical Correlation with Improving Transcranial Doppler Hemodynamics

Streptococcus pneumoniae are Gram-positive bacteria that are responsible for many types of illnesses including pneumonia, sinus infections, and community-acquired meningitis. One important complication of bacterial meningitis is intracranial vasculopathy. Possible etiologies include vasculitis, vasospasm, endocarditis, or intra-arterial thrombosis. We present a case report of S. pneumoniae meningitis treated with antibiotics in which clinical improvement correlated with serial transcranial Doppler ultrasonography (TCD) improvement, suggesting vasospasm or vasculitis as a possible mechanism for intracranial vasculopathy.
Acid Degradable and Biocompatible Polymeric Nanoparticles for the Potential Codelivery of Therapeutic Agents

The synthesis of well-defined functional nanoparticles for the encapsulation of hydrophobic and hydrophilic drugs is described. Nanoparticles were built from amphiphilic copolymers consisting of P(OEG-A) homopolymers chain extended with vinyl benzyl chloride (VBC) and pentafluorophenyl acrylate (PFP-A) comonomers. Subsequently, the pendant chlorine atoms, introduced into the chains by VBC units, were substituted using sodium methanethiosulfonate, yielding copolymer chains with methanethiosulfonate (MTS) pendant functionality. The thiol/MTS exchange chemistry afforded by the MTS groups was then used to introduce different functional groups by reacting with a range of thiols. These copolymers were self-assembled in water yielding nanoparticles with sizes of ∼20 nm. The activated esters in the copolymer were used to cross-link the nanoparticles with difunctional amino compounds (cross-linkers). A cross-linker bearing an acid cleavable bond (ketal) was used to generate pH-sensitive core–shell nanoparticles. D.
Resting and field metabolic rates of Awassi sheep and Baladi goats raised by Negev bedouin

Abstract Sheep are grazers and goats are intermediate feeders. By employing O2 consumption and heart rate measurements, resting metabolic rate (RMR) and field metabolic rate (FMR) were determined in four male fat-tailed Awassi sheep (44.0 ± 3.94) and four male Baladi goats (35.5 ± 5.42 kg) that were co-grazing natural pasture in the Negev Desert. There were 67.7 ± 3.75 g DM/m2 of herbaceous vegetation biomass, which was rapidly becoming senescent and more fibrous. We hypothesized that FMR of these desert-adapted ruminants would be relatively low when compared to other sheep and goat breeds, as animals in arid areas tend to have low metabolic rates. Both sheep (n = 6) and goats (n = 6) foraged 71% of the allotted 11 h free-pasture period; however, sheep grazed more than goats (P < 0.001); whereas goats browsed more than sheep (P < 0.001). RMR was higher (P = 0.007) in sheep than in goats (529 ± 23.5 v. 474 ± 25.4 kJ/kg0.75 BW/d), but FMR did not differ between species (618 ± 55.7 v. 613 ± 115.2 kJ/kg0.75 BW/d). In addition, the cost of activities, as a proportion of FMR, did not differ between sheep and goats; FMR increased by 89 kJ/kg0.75 BW/d or 17% in sheep and by 138 kJ/kg0.75 BW/d or 29% in goats. In comparing FMRs of sheep and goats in this study with these species in other studies, differences were inconsistent and, therefore, our hypothesis was not supported.
A new spin on special relativity

Magnetic domain walls have their own speed limit More than a decade ago, weak magnetic fluctuations called spin waves were found to undergo the Doppler effect in magnetic wires (1). That experiment demonstrated that spin waves obey a version of Galilean relativity. This relativity is not the kind that we experience, but an emergent instance embedded within the spin waves' own magnetic realm. On page 1438 of this issue, Caretta et al. (2) show that domain walls, or twists in a material's magnetization, obey not only Galilean relativity but also Einsteinian special relativity. The authors experimentally demonstrate that domain walls possess fundamental velocity limits corresponding not to the speed of light but instead to the limiting speed of high-energy spin waves.
Direct observation of Klein tunneling in phononic crystals

A sound demonstration of Klein tunneling The ability of particles to tunnel through barriers is an important property of quantum mechanical systems, and the extent of the effect is strongly dependent on the properties of the barrier. By contrast, Klein tunneling can exhibit unity transmission that is independent of the width and height of the energy barrier, but direct evidence for this effect remains elusive. Using a phononic system comprising a periodic array of dielectric pillars, Jiang et al. provide evidence for the direct observation of Klein tunneling. Near-unity transmission of acoustic excitations was observed across the barrier independently of its width and height. This ability to tune the effect by controlling the size of the junctions and the frequency of incident waves provides a promising platform to explore complex nontrivial physics and applications in signal processing and information communications. Science, this issue p. 1447 Near-unity tunneling transmission is observed for acoustic excitations independent of the barrier properties. Tunneling plays an essential role in many branches of physics and has found important applications. It is theoretically proposed that Klein tunneling occurs when, under normal incidence, quasiparticles exhibit unimpeded penetration through potential barriers independent of their height and width. We created a phononic heterojunction by sandwiching two types of artificial phononic crystals with different Dirac point energies. The direct observation of Klein tunneling as shown by the key feature of unity transmission is demonstrated. Our experiment reveals that Klein tunneling occurs over a broad band of acoustic frequency. The direct observation of Klein tunneling in phononic crystals could find applications in signal processing, supercollimated beams, and communications.
Electron density of an individual microdischarge channel in patterns in a dielectric barrier discharge at atmospheric pressure

The electron density of an individual microdischarge channel in different stable patterns including a square and a hexagon pattern in a dielectric barrier discharge in argon at atmospheric pressure is investigated using a spectral line profile method. The procedure for deconvolution of the asymmetric convolution integral is used to obtain the Stark broadening and shift of Ar I 696.54 nm for the calculation of electron density. The broadening parameters such as electron impact width ωe and ion impact width α can also be obtained from the procedure. By comparing ωe with the theoretical values at different electron temperatures given by Griem, the electron temperature can be reasonably estimated. It is found that the electron density in an individual microdischarge channel increases with increasing voltage.
Low Cerebrospinal Fluid Levels of Hemopexin Are Associated With Increased Alzheimer's Pathology, Hippocampal Hypometabolism, and Cognitive Decline

Brain iron dyshomeostasis is a feature of Alzheimer's disease. Conventionally, research has focused on non-heme iron although degradation of heme from hemoglobin subunits can generate iron to augment the redox-active iron pool. Hemopexin both detoxifies heme to maintain iron homeostasis and bolsters antioxidant capacity via catabolic products, biliverdin and carbon monoxide to combat iron-mediated lipid peroxidation. The aim of the present study was to examine the association of cerebrospinal fluid levels (CSF) hemopexin and hemoglobin subunits (α and β) to Alzheimer's pathological proteins (amyloid and tau), hippocampal volume and metabolism, and cognitive performance. We analyzed baseline CSF heme/iron proteins (multiplexed mass spectrometry-based assay), amyloid and tau (Luminex platform), baseline/longitudinal neuroimaging (MRI, FDG-PET) and cognitive outcomes in 86 cognitively normal, 135 mild-cognitive impairment and 66 Alzheimer's participants from the Alzheimer's Disease Neuroimaging Initiative-1 (ADNI-1) cohort. Multivariate regression analysis was performed to delineate differences in CSF proteins between diagnosis groups and evaluated their association to amyloid and tau, neuroimaging and cognition. A p-value ≤ 0.05 was considered significant. Higher hemopexin was associated with higher CSF amyloid (implying decreased brain amyloid deposition), improved hippocampal metabolism and cognitive performance. Meanwhile, hemoglobin subunits were associated with increased CSF tau (implying increased brain tau deposition). When dichotomizing individuals with mild-cognitive impairment into stable and converters to Alzheimer's disease, significantly higher baseline hemoglobin subunits were observed in the converters compared to non-converters. Heme/iron dyshomeostasis is an early and crucial event in AD pathophysiology, which warrants further investigation as a potential therapeutic target.
A Dual-Crosslinked and Anisotropic Regenerated Cellulose/Boron Nitride Nanosheets Film With High Thermal Conductivity, Mechanical Strength, and Toughness

The highly thermo-conductive but electrically insulating film, with desirable mechanical performances, is extremely demanded for thermal management of portable and wearable electronics. The integration of boron nitride nanosheets (BNNSs) with regenerated cellulose (RC) is a sustainable strategy to satisfy these requirements, while its practical application is still restricted by the brittle fracture and loss of toughness of the composite films especially at the high BNNS addition. Herein, a dual-crosslinked strategy accompanied with uniaxial pre-stretching treatment was introduced to engineer the artificial RC/BNNS film, in which partial chemical bonding interactions enable the effective interfiber slippage and prevent any mechanical fracture, while non-covalent hydrogen bonding interactions serve as the sacrifice bonds to dissipate the stress energy, resulting in a simultaneous high mechanical strength (103.4 MPa) and toughness (10.2 MJ/m3) at the BNNS content of 45 wt%. More importantly, attributed to the highly anisotropic configuration of BNNS, the RC/BNNS composite film also behaves as an extraordinary in-plane thermal conductivity of 15.2 W/m·K. Along with additional favorable water resistance and bending tolerance, this tactfully engineered film ensures promised applications for heat dissipation in powerful electronic devices.
Identification MdeSOS1 in Magnolia denudata and its function in response to salt stress

ABSTRACT In this study, annual Magnolia denudata seedlings were treated with a 200 mmol L−1 NaCl solution. Na+ content in its stems increased by more than about 24 times after 72 h and K+ content in leaves basically maintained in a steady state. MdeSOS1, isolated from M. denudata, comprised a 3453-bp ORF and included 12 transmembrane structures within its N terminal and a hydrophilic tail in its C-terminal. Its protein shared the identity of 68.3% and 62.7% at the peptide level with the homologue PeSOS1 and AtSOS1 respectively. The MdeSOS1 was significantly induced to up-regulation in various tissues exposed to salt stress and improved the salt tolerance of Arabidopsis. Our results also revealed that the MdeSOS1-GFP fusion protein was located on the plasma membrane and MdeSOS1 encoded a salt-inducible plasma membrane Na+/H+ antiporter, which provides a reference to improve the salt tolerance of Magnolia species by transgenic approaches.
Time of Day Matters: An Exploratory Assessment of Chronotype in a Forensic Psychiatric Hospital

A growing body of evidence links the late chronotype to mental illness, aggression, and aversive personality traits. However, much of what we know about these associations is based on healthy cohorts, and it is unclear how individuals with high levels of aggression, including forensic psychiatric populations, but not offenders, are affected. The present study aimed to measure chronotype in a forensic psychiatric inpatient population, evaluate the impact of diagnosis, and identify any interactive relationships between chronotype, diagnosis, aggression, and dark triad traits. Subjects completed the reduced Morningness–Eveningness Questionnaire (rMEQ), Munich ChronoType Questionnaire (MCTQ), Pittsburgh Sleep Quality Index (PSQI), Buss Perry Aggression Questionnaire–Short Form (BPAQ-SF), and Short Dark Triad Questionnaire (SD3). We sampled 55 forensic psychiatric patients (52 males) between the ages of 23 and 73 years (mean ± SD: 39.6 ± 14.3 years). Among the patients sampled, 25% were evening types and 36% were morning types. Eveningness was greater in patients with a personality disorder; however, no chronotype differences were found for psychosis patients. Patients without psychosis had a positive association between anger and eveningness, as well as between hostility and eveningness. For subjects with a substance use disorder, morningness was positively associated with narcissism. Conversely, an association between eveningness and greater narcissism was identified in patients who did not have a substance use disorder. These findings suggest that, compared to the general population, evening types are more prevalent in forensic psychiatric populations, with the strongest preference among patients diagnosed with a personality disorder. No differences in chronotype were identified for psychosis patients, which may be related to anti-psychotic medication dosing. Given the sex distribution of the sample, these findings may be more relevant to male populations.
Molecular dynamics simulations of hydrogen adsorption/desorption by palladium decorated single-walled carbon nanotube bundle

Utilising molecular dynamics simulations, the hydrogen molecules adsorption isotherms of the (8, 0) palladium decorated single-walled carbon nanotube (SWNT) were obtained. The hydrogen adsorption was studied on the external, interstial and internal surfaces of the SWNT bundle at several temperatures ranging from 77 to 400 K. The results were compared with the bare single-walled carbon nanotube bundle under the same conditions. The decorated carbon nanotube bundle hydrogen adsorption was significantly higher than that of the bare one. The hydrogen desorption and readsorption were studied using temperature as the readsorption/desorption variable. The rate constants were calculated for the hydrogen desorption at different temperatures. The calculated decorated SWNT bundle hydrogen desorption activation energy was higher than that for the bare SWNT bundle. The calculated activation energies for the hydrogen desorption in both nanotube bundles specified the temperature dependency of hydrogen desorption.
Using Intervention Mapping to Develop a Provider Intervention to Increase HPV Vaccination in a Federally Qualified Health Center

Introduction: A healthcare provider's ability to give a strong recommendation for the HPV vaccine is of utmost importance in increasing HPV vaccination. To reduce the burden of HPV-related cancers, there is a critical need to develop and implement theory-based interventions aimed at strengthening healthcare providers' communication about the HPV vaccine. Methods: We used Intervention Mapping (IM) steps 1–5 to develop and implement a provider-level intervention that aligns with the priorities and needs of a large, urban Federally Qualified Health Center (FQHC). Results: In step 1, a diverse planning group identified barriers to HPV vaccination in clinical settings and generated process maps and a logic model of the problem. Step 2 outlined outcomes and provider performance objectives of the intervention and identified knowledge, skills, self-efficacy, outcome expectations, and normative beliefs as modifiable targets that need to change for providers to deliver strong recommendations for the HPV vaccine to parents and patients. In step 3, the planning group mapped the methods of persuasive communication, information, and modeling and skills training to behavioral targets and outlined the program practical applications (strategies) components, scope, and sequence. In steps 4 and 5, the planning group produced the intervention and planned for program implementation. The iterative and participatory process of IM resulted in modifications to the initial intervention that aligned with the needs of the FQHC. Discussion: IM provided a systematic, participatory, and iterative approach for developing a theory-based provider-level intervention aimed at strengthening healthcare providers' ability to provide a strong recommendation for the HPV vaccine to eligible patients and parents served by a large FQHC. IM assisted with the identification of behavioral targets and methods that move beyond HPV knowledge and reminders to create behavior change. IM can help researchers and planners describe the processes and rational behind developing interventions and may help to facilitate implementation in real-world clinical settings by tailoring intervention components to the needs of the population.