Miracle-dz/UniFAR-FTUs huggingface dataset:
Trabecular architecture of the distal femur in extant hominids.

Extant great apes are characterized by a wide range of locomotor, postural and manipulative behaviours that each require the limbs to be used in different ways. In addition to external bone morphology, comparative investigation of trabecular bone, which (re-)models to reflect loads incurred during life, can provide novel insights into bone functional adaptation. Here, we use canonical holistic morphometric analysis (cHMA) to analyse the trabecular morphology in the distal femoral epiphysis of Homo sapiens (n = 26), Gorilla gorilla (n = 14), Pan troglodytes (n = 15) and Pongo sp. (n = 9). We test two predictions: (1) that differing locomotor behaviours will be reflected in differing trabecular architecture of the distal femur across Homo, Pan, Gorilla and Pongo; (2) that trabecular architecture will significantly differ between male and female Gorilla due to their different levels of arboreality but not between male and female Pan or Homo based on previous studies of locomotor behaviours. Results indicate that trabecular architecture differs among extant great apes based on their locomotor repertoires. The relative bone volume and degree of anisotropy patterns found reflect habitual use of extended knee postures during bipedalism in Homo, and habitual use of flexed knee posture during terrestrial and arboreal locomotion in Pan and Gorilla. Trabecular architecture in Pongo is consistent with a highly mobile knee joint that may vary in posture from extension to full flexion. Within Gorilla, trabecular architecture suggests a different loading of knee in extension/flexion between females and males, but no sex differences were found in Pan or Homo, supporting our predictions. Inter- and intra-specific variation in trabecular architecture of distal femur provides a comparative context to interpret knee postures and, in turn, locomotor behaviours in fossil hominins.
Analysis of the Physical Activity Levels and Literacy of Grand Valley State University Students

Introduction: It’s been said that students with higher physical activity (PA) levels, tend to get better grades in school. The research behind this topic is mixed, with most regarding children, not college-aged adults. Methods: A PA health questionnaire was designed in a similar format as a survey given by the Centers for Disease Control (CDC). The survey was voluntarily filled out by 94 randomly selected Grand Valley State University (GVSU) students. Results: No significant differences were found between PA levels and GPA or major of GVSU students. Significant differences were found between the American Heart Association’s (AHA) guidelines for PA, and the predicted amount of PA needed for adults by the GVSU students. Conclusion: The significant difference in predicted and actual guideline’s PA shows a need to improve their physical health literacy. High variance in the data also suggests that students are not getting enough PA, if any at all.
Comparison of the Fixation Strengths of Screws between the Traditional Trajectory and the Single and Double Endplate Penetrating Screw Trajectories Using Osteoporotic Vertebral Body Models Based on the Finite Element Method

Study Design This is a finite element (FE) study. Purpose To compare the fixation strength of traditional trajectory (TT) and single and double endplate penetrating screw trajectories (SEPST/DEPST) to the osteoporotic vertebral body model based on the FE method. Overview of Literature SEPST/DEPST have been developed to enhance the fixation strength in patients with diffuse idiopathic hyperostosis (DISH). This technique was also applied to patients with osteoporosis. However, determining the superiority of SEPST/DEPST is difficult because of the heterogeneous patient backgrounds. Methods Twenty vertebrae (T12 and L1) from 10 patients with osteoporosis (two males and eight females; mean age, 74.7 years) were obtained to create the 10 FE models. First, a single screw was placed with TT and SEPST/DEPST, and the fixation strength was compared by axial pullout strength (POS) and multidirectional loading tests. Second, two screws were placed on the bilateral pedicles with TT and SEPST/DEPST, and the fixation force of the vertebrae in the constructs in flexion, extension, lateral flexion, and axial rotation was examined. Results SEPST and DEPST had 140% and 171% higher POS values than TT, respectively, and the DEPST result was statistically significant (p=0.007). The multidirectional fixation strength was significantly higher in DEPST and SEPST than in TT in the cranial, caudal, and medial directions (p<0.05) but not in the lateral direction (p=0.05). The vertebral fracture strength at the lower instrumented vertebra of the DEPST tended to be higher than that of TT. The vertebral motion angles in SEPST and DEPST were significantly smaller in lateral bending (p=0.02) and tended to be smaller in flexion and extension than in TT (p=0.13). Conclusions This study may provide useful information for spine surgeons in deciding whether to choose the SEPS or DEPS technique for augmenting fixation in osteoporotic vertebral fracture surgery.
Informed development of a multi-species biofilm in chronic obstructive pulmonary disease.

Recent evidence indicates that microbial biofilm aggregates inhabit the lungs of COPD patients and actively contribute towards chronic colonization and repeat infections. However, there are no contextually relevant complex biofilm models for COPD research. In this study, a meta-analysis of the lung microbiome in COPD was used to inform development of an optimized biofilm model composed of genera highly associated with COPD. Bioinformatic analysis showed that although diversity matrices of COPD microbiomes were similar to healthy controls, and internal compositions made it possible to accurately differentiate between these cohorts (AUC = 0.939). Genera that best defined these patients included Haemophilus, Moraxella and Streptococcus. Many studies fail to account for fungi; therefore, Candida albicans was included in the creation of an interkingdom biofilm model. These organisms formed a biofilm capable of tolerating high concentrations of antimicrobial therapies with no significant reductions in viability. However, combined therapies of antibiotics and an antifungal resulted in significant reductions in viable cells throughout the biofilm (p < 0.05). This biofilm model is representative of the COPD lung microbiome and results from in vitro antimicrobial challenge experiments indicate that targeting both bacteria and fungi in these interkingdom communities will be required for more positive clinical outcomes.
The global RNA–RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

Significance Albeit it has long been known that the RNA chaperone Hfq is critical for Klebsiella pneumoniae virulence and adaptation to various environmental stress conditions, the landscape of Hfq-associated transcripts in this organism has not been explored. In a global search for RNA–RNA interactions, we annotated targets of conserved as well as previously unknown regulatory RNAs. We show that a Klebsiella-specific sRNA (small regulatory RNA), termed DinR, contributes to inhibition of cell cycle progression in the response to DNA damage by interfering with translation of the essential divisome component FtsZ. Acting at the posttranscriptional level, DinR complements other conserved mechanisms of FtsZ deactivation in the SOS response and fosters filamentation of K. pneumoniae.
Telomere length and TERT polymorphisms as biomarkers in asbestos-related diseases

Abstract Background Asbestos exposure has been proposed as a risk factor for shorter telomere length. The aim of our study was to investigate whether telomere length in leukocytes and hTERT genetic polymorphisms may serve as potential biomarkers for the risk of developing asbestos-related diseases and as biomarkers of progression and chemotherapy response rate in malignant mesothelioma (MM). Subjects and methods We conducted two retrospective studies. In the first study, a case-control study, telomere length and hTERT polymorphisms were determined in patients with MM, subjects with pleural plaques and controls without the asbestos related disease, who were occupationally exposed to asbestos. In the second study, a longitudinal observational study, telomere length was also determined in samples from MM patients before and after chemotherapy. Telomere length was determined by monochromatic multiplex quantitative polymerase chain reaction (PCR), while competitive allele-specific PCR was used to genotype hTERT rs10069690, rs2736100 and rs2736098. Logistic regression and survival analysis were used in statistical analysis. Results Patients with MM had shorter telomere length than subjects with pleural plaques (p < 0.001). After adjustment for age, rs2736098 CT, and rs10069690 TT and CT+TT genotypes were significantly associated with a higher risk of MM (padj = 0.023; padj = 0.026 and padj = 0.017), while rs2736100 AA and CA+AA genotypes conferred to a lower risk for MM compared to all other subjects (padj = 0.017, and padj = 0.026). Telomere length was not associated with a response to chemotherapy (p > 0.05) or time to disease progression (p > 0.05). Carriers of one or two polymorphic rs10069690 T alleles had a good response to chemotherapy (p = 0.039, and p = 0.048), these associations remained statistically significant after adjustment for age (padj = 0.019; padj = 0.017). Carriers of two polymorphic rs2736100 A alleles had a longer time to disease progression (p = 0.038). Conclusions Shorter telomere length and hTERT polymorphisms may serve as a biomarker for the risk of developing MM. Additionally, rs10069690 and rs2736100 polymorphisms, but not telomere length, were associated with a chemotherapy response or MM progression.
Effect of rumen-protected choline on fat digestibility and lymph metabolome in dairy cows.

Objectives were to determine the effects of supplementing rumen-protected choline (RPC) from an established source with low (L, 28.8%) or a prototype with less lipid coating protection and high (H, 60.0%) concentrations of choline chloride on digestibility of fat and supra-mammary lymph metabolome in feed-restricted cows. Pregnant, nonlactating Holstein cows (n = 33; 11/treatment) at mean (±standard deviation) 231 ± 4.7 days of gestation were blocked by body condition (4.23 ± 0.47) and assigned to receive 0 (CON) or 25.8 g/d of choline ion from L (L25.8) or H (H25.8). Cows were adapted to the diet and then fed-restricted to 42% of the net energy of lactation required for maintenance and pregnancy for 9 days. Intake of metabolizable methionine was maintained at 19 g/d. On Day 9, cows were fed 450 g of saturated fatty acids (SFA), and feces and blood were sampled continuously for 24 h. Supra-mammary lymph was sampled 6 h after feeding SFA and metabolome was characterized. Feeding RPC increased digestibility of fat (CON = 80.4 vs. RPC = 86.0 ± 1.9%) and reduced the concentration of haptoglobin in serum (CON = 174 vs. RPC = 77 ± 14 µg/ml) independent of source of RPC fed. Feeding RPC increased the concentrations of triacylglycerol in serum (CON = 15.1 vs. RPC = 17.8 ± 1.9 mg/dl) in feed-restricted cows after feeding SFA, and the increment tended to be greater for cows fed H25.8 than L25.8. Supplementing RPC tended to increase the concentrations of triacylglycerol (CON = 11.4 vs. RPC = 15.8 ± 3.4 mg/dl) in supra-mammary lymph. Feeding RPC increased the concentration of choline and affected the concentrations of analytes involved in metabolic pathways associated with amino acid metabolism and biosynthesis of phospholipids in lymph compared with CON. Feeding RPC, independent of source used, increased fat digestibility with some changes in lymph metabolome in cows under negative nutrient balance.
3D fracture analyses of various rock samples through x-ray micro-tomography

Hydrocarbon reservoirs are currently declining. Reservoirs are becoming depleted, and production needs to satisfy the demand and supply of hydrocarbons. For tight reservoirs such as shales, fracturing will become the main source of improving the permeability. It is therefore vital to conduct research into the behavior of fractures in the reservoir. The aim is to study how fractures develop in terms of fracture size, coalescence, patterns and in which dimensions they often occur. Often the importance of the behavior of these fractures and their contribution to flow in reservoirs also formed part of this research. In this investigation, the Posidonia shale core was examined using three different layering orientations. The three different layer orientated shale cores were subjected to axial loading in order to induce fracturing. These induced fractures were created in two ways. The first was by axial loading until the core reached maximum failure. The second involved loading in stages and scanning the core after each loading stage in the micro-CT scanner. This procedure was repeated until maximum failure was reached. An Indiana limestone core and sandstone core were also analyzed. The behavior, coalescence, frequently seen fracture patterns, angle with respect to the z-axis and apertures of the fractures were studied and compared. This was performed in both a quantitative and qualitative matter using the commercial Avizo® Fire software at TU Delft. A small part of this study touch on the modeling of the observed shear fracture pattern from a shale core preformed in Abaqus. The results from the fracture analyses shows that the largest fractures are seen in the shale cores, for which the fracture initiation was created by one loading stage until failure. Another observation shows that there is clear set of different fractures that is seen for each distinctive layered core. From the observed patterns a simple 2D simulation is built in Abaqus. From the simulation is seen that for cracks under a certain angle, the master fracture is intersected by a 300 smaller fracture, the results in opening of the master fracture. This is also the case in the 2D slice, which is a representation of the 2D-model fracture configuration.
Factors associated with the cholera outbreak in Al-Mahweet-Yemen: Analytic Study.

INTRODUCTION The emergence of cholera in 2016 in Yemen, worsened the morbidity and mortality of diarrheal diseases, particularly among children under five. Multiple outbreaks in Yemen are triggered by years of conflict and the collapse of basic infrastructure including water supply and sanitation systems. This study aims to assess factors associated with the cholera outbreak, in a cholera-prone region, in Al-Mahweet, Yemen. METHODOLOGY We conducted a multivariate analysis of the data collected through a household survey of 384 households in Al-Mahweet, Yemen. RESULTS Families with children under five years, large households, and those living in Al Mahweet district were associated with a higher incidence of cholera. Water treatment by boiling, filtering, and chlorination as a protective practice against cholera showed a borderline significance, while other WASH practices including regular hand washing, open defection, safe water source, and improved sanitation facilities were statistically insignificant. Community awareness of cholera transmission and prevention measures showed no association with cholera incidence. CONCLUSIONS Findings suggest that living conditions, including large households and lack of access to treated water, increase the risk of cholera. Interventions to increase access to treated water and improve the hygienic conditions of large households are of central importance. Affected communities must receive effective educational campaigns that are adjusted to change hygienic practices and improve knowledge of cholera transmission and protection measures.
Chapter 12 Inner-arc volcanism: Barren and Narcondam islands

Abstract Barren and Narcondam are active and now extinct, respectively, volcanic islands that belong to the inner-arc volcanic belt that extends from Java in the east to Burma in the north. Modern eruptions on Barren Island have been exclusively scoria cone-forming Strombolian-type activity in contrast to historic (1787–32) eruptions that witnessed a switch from scoria cone activity to abundant basaltic lava flows. Prehistoric (late Pleistocene) eruptions were alternating effusive and explosive events. The prehistoric events formed a mafic stratovolcano (island) and the associated large eruptions produced a c. 2.0 km diameter crater at the centre of the stratocone. Barren Island lavas are mainly basalts and basaltic andesites, whereas Narcondam rocks are dacite-andesite-rhyolite and contain evidence of magma mixing of both mantle and crustal material. The types of volcanoes and volcanism associated with Barren and Narcondam have been attributed to differences in tectonic setting and the nature of the basement below the volcanoes. It is likely that continental or transitional crust exists below Narcondam, in contrast to oceanic lithosphere below Barren Island.
A Quantum Chemistry Approach to Linear Vibro-Polaritonic Infrared Spectra with Perturbative Electron–Photon Correlation

In the vibrational strong coupling (VSC) regime, molecular vibrations and resonant low-frequency cavity modes form light–matter hybrid states, vibrational polaritons, with characteristic infrared (IR) spectroscopic signatures. Here, we introduce a molecular quantum chemistry-based computational scheme for linear IR spectra of vibrational polaritons in polyatomic molecules, which perturbatively accounts for nonresonant electron–photon interactions under VSC. Specifically, we formulate a cavity Born–Oppenheimer perturbation theory (CBO-PT) linear response approach, which provides an approximate but systematic description of such electron–photon correlation effects in VSC scenarios while relying on molecular ab initio quantum chemistry methods. We identify relevant electron–photon correlation effects at the second order of CBO-PT, which manifest as static polarizability-dependent Hessian corrections and an emerging polarizability-dependent cavity intensity component providing access to transmission spectra commonly measured in vibro-polaritonic chemistry. Illustratively, we address electron–photon correlation effects perturbatively in IR spectra of CO2 and Fe(CO)5 vibro-polaritonic models in sound agreement with nonperturbative CBO linear response theory.
Sustained attention and the flash grab effect

When a stationary target is briefly presented on top of a moving background as it reverses direction, the target is displaced perceptually in the direction of the upcoming motion (the flash grab effect). To determine the role of attention in this effect, we investigated whether the predictability of the location of the flash grab target modulates the illusion. First, we established that effect was weaker for spatially predictable targets. Next, we showed that the flash grab effect decreased for a narrower spatial spread of attention before the onset of the target and that it was smaller for left hemifield presentations than right. Finally, we demonstrated that diverting attention away from the target and the background motion decreases the flash grab effect. In the first two experiments, the decrease in the illusion could be attributed to either increased attention to the target or decreased attention to the motion; we assume that increasing attention to the target necessarily decreases attention to the motion. However, in the final experiment, the central task decreases attention to both the target and the motion. The results show a decrease in the illusion and that reveals that attention to the motion is the primary causal factor.
The end of growth

We live in a world with ever-increasing levels of financial debt—public and private. We are also depleting the earth’s natural resources, including fresh water, fertile soil, forests, marine ecosystems, biodiversity, fossil fuels, minerals, and pollution sinks. Since debt represents a promise of future repayment of labor and resources the book argues it is inevitable that the aggregate promises to repay will eventually exceed the available resources for repayment. In fact, that may have already have happened.
Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

ABSTRACT Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%–50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.