Miracle-dz/UniFAR-FTUs huggingface dataset:
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource. ’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.
Urinary liver‐type fatty acid‐binding protein in clinically healthy elderly cats: Evaluation of its potential to detect IRIS stage 1 chronic kidney disease and borderline proteinuria

Abstract Background Urinary liver‐type fatty acid‐binding protein (uL‐FABP) is a promising biomarker to detect early chronic kidney disease (CKD) in cats. Few healthy cats show increased uL‐FABP for unknown reasons. Objectives The objective of this study was to evaluate uL‐FABP in a large healthy elderly cat population comparing cats with and without International Renal Interest Society (IRIS) stage 1 CKD and with and without borderline proteinuria. Methods This was a cross‐sectional study. One hundred ninety‐six clinically healthy client‐owned cats of ≥7 years old were subdivided based on two criteria: (1) having either IRIS stage 1 CKD or no evidence of CKD and (2) having borderline proteinuria or no proteinuria. Urinary L‐FABP was measured using a validated commercially available feline L‐FABP ELISA. Results Overall, uL‐FABP was detectable in 6/196 (3%) healthy elderly cats. For the first subdivision, nine (5%) cats had IRIS stage 1 CKD, 184 cats had no evidence CKD and three cats were excluded. All cats with IRIS stage 1 CKD had uL‐FABP concentrations below the detection limit, whereas 6/184 (3%) cats without IRIS stage 1 CKD had detectable uL‐FABP concentrations (median 1.79 ng/ml, range 0.79–3.66 ng/ml). For the second subdivision, 47 (24%) cats had borderline proteinuria, 147 cats had no proteinuria and two cats were excluded. One of the borderline proteinuric cats had a detectable uL‐FABP concentration, whereas the other five cats with detectable uL‐FABP concentrations were non‐proteinuric. Conclusion With the current assay, the screening potential of uL‐FABP as an early biomarker for feline CKD is limited as uL‐FABP was rarely detected in clinically healthy elderly cats independently of the presence of either IRIS stage 1 CKD or borderline proteinuria.
Gsk3β regulates the resolution of liver ischemia/reperfusion injury via MerTK

Although glycogen synthase kinase β (Gsk3β) has been shown to regulate tissue inflammation, whether and how it regulates inflammation resolution versus inflammation activation is unclear. In a murine liver, partial warm ischemia/reperfusion injury (IRI) model, we found that Gsk3β inhibitory phosphorylation increased at both the early-activation and late-resolution stages of the disease. Myeloid Gsk3β deficiency not only alleviated liver injuries, it also facilitated the restoration of liver homeostasis. Depletion of Kupffer cells prior to the onset of liver ischemia diminished the differences between the WT and Gsk3β-KO mice in the activation of liver IRI. However, the resolution of liver IRI remained accelerated in Gsk3β-KO mice. In CD11b-DTR mice, Gsk3β-deficient BM-derived macrophages (BMMs) facilitated the resolution of liver IRI as compared with WT cells. Furthermore, Gsk3β deficiency promoted the reparative phenotype differentiation in vivo in liver-infiltrating macrophages and in vitro in BMMs. Gsk3 pharmacological inhibition promoted the resolution of liver IRI in WT, but not myeloid MerTK-deficient, mice. Thus, Gsk3β regulates liver IRI at both activation and resolution stages of the disease. Gsk3 inactivation enhances the proresolving function of liver-infiltrating macrophages in an MerTK-dependent manner.
Embeddings of Riemannian Manifolds with Heat Kernels and Eigenfunctions

We show that any closed n‐dimensional Riemannian manifold can be embedded by a map constructed from heat kernels at a certain time from a finite number of points. Both this time and this number can be bounded in terms of the dimension, a lower bound on the Ricci curvature, the injectivity radius, and the volume. It follows that the manifold can be embedded by a finite number of eigenfunctions of the Laplace operator. Again, this number only depends on the geometric bounds and the dimension. In addition, both maps can be made arbitrarily close to an isometry. In the appendix, we derive quantitative estimates of the harmonic radius, so that the estimates on the number of eigenfunctions or heat kernels needed can be made quantitative as well. © 2016 Wiley Periodicals, Inc.
Perilla frutescens L. alleviates trimethylamine N‐oxide–induced apoptosis in the renal tubule by regulating ASK1‐JNK phosphorylation

Trimethylamine N‐oxide (TMAO) is associated with overall mortality in patients with chronic kidney disease (CKD). Previous findings suggest that P. frutescens (L.) can alleviate renal injury, but its effects and mechanisms underlying alleviation of TMAO‐induced kidney damage remain unclear. In this study, a TMAO injury model, in vivo and in vitro, was established to clarify the effects and mechanisms of P. frutescens in alleviating TMAO‐induced kidney injury. The results show that TMAO (60 mM/L) can induce the activation of apoptosis signal‐regulating kinase 1 (ASK1)‐c‐Jun N‐terminal kinase (JNK), thus aggravating downstream cell apoptosis in vitro. The study also found that P. frutescens aqueous extract (PFAE) (5 mg/mL) can inhibit TMAO‐induced apoptosis by downregulating ASK1‐JNK phosphorylation. In the in vivo experiments, it was demonstrated that TMAO can increase the levels of blood urea nitrogen and cystatin C, aggravating renal tubular epithelial apoptosis. The results also show that PFAE can reduce TMAO‐induced renal damage by inhibiting ASK1‐JNK phosphorylation in vivo. Our findings confirmed that P. frutescens can alleviate TMAO‐induced renal tubule apoptosis by regulating ASK1‐JNK phosphorylation, indicating that P. frutescens may be an effective treatment for alleviating TMAO damage in CKD.
New Bounds on van der Waerden-type Numbers for Generalized 3-term Arithmetic Progressions

AbstractLet aand bbe positive integers with a≤ b. An (a,b)-triple is a set {x,ax+d,bx+2d}, where x,d≥ 1. Deﬁne T(a,b;r) to be the least positive integer nsuch that anyr-coloring of {1,2,. ,n} contains a monochromatic (a,b)-triple. Earlier results gavean upper bound on T(a,b;2) that is a fourth degree polynomial in b and a, and aquadratic lower bound. A new upper bound for T(a,b;2) is given that is a quadratic.Additionally, lower bounds are given for the case in which a= b, updated tables areprovided, and open questions are presented. 2010 Mathematics subject classiﬁcation: primary 05D10.Keywords and phrases: van der Waerden’s theorem, arithmetic progression, Rado’s theorem,monochromatic sequence. 1 Introduction Van der Waerden [10] proved that for any positive integers n and r, there is a least positiveinteger w(n;r) such that every r-coloring of {1,2,. ,w(n;r)} admits a monochromatic n-term arithmetic progression. The estimation of the function w(n;r) is a notoriously diﬃcultproblem ofRamsey theory. Numerous results analogoustovander Waerden’s theorem, wherethe family of arithmetic progressions is replaced by other families, have been considered.Ramsey properties for a variety of such families, along with a summary of what is known
Minimum 3-year experience with vertebral body tethering for treating scoliosis: A systematic review and single-arm meta-analysis

Purpose Over the past 12 years, vertebral body tethering (VBT) has been gradually promoted for treating scoliosis, but there are few published studies, with only short-term follow-up. This study aimed to systematically review VBT efficacy and safety for treating scoliosis. Methods PubMed, Web of Science, Embase, and the Cochrane Library were searched for studies on VBT treatment of scoliosis published up to November 2021. Two researchers independently screened the literature, extracted data, and assessed the risk of bias in included studies. Data on clinical efficacy, unplanned reoperations, and complications were extracted. The meta-analysis was performed with R 4.1. 0. Results Twenty-six studies involving 1045 patients were included in the meta-analysis. The correction rate of major curve immediately post-operation was 46.6% ± 13.8% (16%–69%) and that at final follow-up was 53.2% ± 17.9% (16%–79%). The single-arm meta-analysis results of all included studies showed that VBT was effective in general. The overall clinical success rate was 73.02% (95% confidence interval [CI]: 68.31%–78.05%). The pooled overall unplanned reoperation rate was 8.66% (95% CI: 5.53%–13.31%). The overall incidence rate of complications was 36.8% (95% CI: 23.9%–49.7%). The subgroup analysis based on follow-up time indicated that patients with follow-up time >36 months had increased clinical success rate, unplanned reoperation rate, and incidence rate of complications compared with those with <36 months’ follow-up time. The preliminary results showed that after 36 months of follow-up, only 7.17% (95% CI: 4.81%–10.55%) of patients required posterior spinal fusion (PSF) surgery and nearly 93% of patients avoided spinal fusion surgeries. Conclusions The current evidence from at least 3-year follow-up in different countries indicates that VBT is an effective surgical approach for treating scoliosis, with 73.88% of patients achieving clinical success. Nevertheless, about one in seven patients (15.8%) required unplanned reoperations, but only 7.17% required PSF. About half (52.17%) of the patients experienced complications. Due to the limitation of the study number and quality, our conclusion may be biased and requires verification by further studies with longer follow-up times.
An analysis of the relationship between microneedle spacing, needle force and skin strain during the indentation phase prior to skin penetration

Abstract Microneedle (MN) array patches present a promising new approach for the minimally invasive delivery of therapeutics and vaccines. However, ensuring reproducible insertion of MNs into the skin is challenging. The spacing and arrangement of MNs in an array are critical determinants of skin penetration and the mechanical integrity of the MNs. In this work, the finite element method was used to model the effect of MN spacing on needle reaction force and skin strain during the indentation phase prior to skin penetration. Spacings smaller than 2–3 mm (depending on variables, e.g., skin stretch) were found to significantly increase these parameters.
Decay of Mean Values of Multiplicative Functions

Abstract For given multiplicative function $f$ , with $\left| f\left( n \right) \right|\le 1$ for all $n$ , we are interested in how fast its mean value $\left( 1/x \right)\sum{_{n\le x}f\left( n \right)}$ converges. Halász showed that this depends on the minimum $M\,\left( \text{over}\,y\,\in \,\mathbb{R} \right)\,\text{of}\,\sum{_{p\le x}\left( 1-\operatorname{Re}\left( f\left( p \right){{p}^{-iy}} \right) \right)}/p$ , and subsequent authors gave the upper bound $\ll \left( 1+M \right){{e}^{-M}}$ . For many applications it is necessary to have explicit constants in this and various related bounds, and we provide these via our own variant of the Halász-Montgomery lemma (in fact the constant we give is best possible up to a factor of 10). We also develop a new type of hybrid bound in terms of the location of the absolute value of $y$ that minimizes the sum above. As one application we give bounds for the least representatives of the cosets of the $k$ -th powers mod $p$ .
Protecting the gains: analysis of HIV treatment and service delivery programme data and interventions implemented in 19 African countries during COVID‐19

The potential disruption in antiretroviral therapy (ART) services in Africa at the start of the COVID‐19 pandemic raised concern for increased morbidity and mortality among people living with HIV (PLHIV). We describe HIV treatment trends before and during the pandemic and interventions implemented to mitigate COVID‐19 impact among countries supported by the US Centers for Disease Control and Prevention (CDC) through the President's Emergency Plan for AIDS Relief (PEPFAR).
Targeting glutaminase is therapeutically effective in ibrutinib-resistant mantle cell lymphoma

Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma characterized by frequent relapses. The development of resistance to ibrutinib therapy remains a major challenge in MCL. We previously showed that glutaminolysis is associated with resistance to ibrutinib. In this study, we confirmed that glutaminase (GLS), the first enzyme in glutaminolysis, is overexpressed in ibrutinib-resistant MCL cells, and that its expression correlates well with elevated glutamine dependency and glutaminolysis. Furthermore, we discovered that GLS expression correlates with MYC expression and the functioning of the glutamine transporter ASCT2. Depletion of glutamine or GLS significantly reduced cell growth, while GLS overexpression enhanced glutamine dependency and ibrutinib resistance. Consistent with this, GLS inhibition by its specific inhibitor telaglenastat suppressed MCL cell growth both in vitro and in vivo. Moreover, telaglenastat showed anti-MCL synergy when combined with ibrutinib or venetoclax in vitro, which was confirmed using an MCL patient-derived xenograft model. Our study provides the first evidence that targeting GLS with telaglenastat, alone or in combination with ibrutinib or venetoclax, is a promising strategy to overcome ibrutinib resistance in MCL.
Estimating 3D supraspinatus intramuscular fatty infiltration in older adults: a pilot study

Background A recent report suggests that semi-quantitative two-dimensional Goutallier grade (2D-GG) correlates poorly with quantitative three-dimensional Dixon fat fraction (3D-Dixon-FF) on magnetic resonance imaging (MRI). Purpose To determine whether the finding of poor correlation of supraspinatus 3D-Dixon-FF with 2D-GG is reproducible, and to determine the strength of the correlation of 3D-Dixon-FF with quantitative 2D Dixon fat fraction (2D-Dixon-FF). Material and Methods Ten adults aged ≥60 years were recruited prospectively received shoulder MRI. 2D-Dixon-FF and 3D-Dixon-FF were measured on 6-point Dixon fat fraction maps. 2D-GG was rated on T1-weighted images. Results The mean age of participants was 70.7 ± 3.7 years. The mean 3D-Dixon-FF was 8.3% ± 5.7%; the mean 2D-Dixon-FF was 7.3% ± 4.4%; and the mean 2D-GG was 0.9 ± 0.7. There was a strong correlation for 3D-Dixon-FF with 2D-Dixon-FF (rho = 0.90; P < 0.001) and with 2D-GG (rho = 0.73; P = 0.017). Excellent inter-observer reliability was found for Dixon fat fraction (intraclass correlation coefficient = 0.946), which was good for Goutallier grade (weighted kappa = 0.634). Conclusion Supraspinatus 3D-Dixon-FF had a strong correlation with 2D-Dixon-FF and 2D-GG in our study population.
Photodynamic therapy in the treatment of condyloma acuminata: A systematic review of clinical trials

Introduction Condylomata acuminata (CA) is a sexually transmitted infection with a high prevalence associated with psychosexual morbidity in both men and women of various age. Up to now, treatment modalities yield low clearance and recurrence rate (RR) and are also deemed low quality evidence-wise. Photodynamic therapy (PDT) is a novel and promising therapy to effectively cure and prevent CA recurrence. Method This systematic review was reported according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) and registered to the International Prospective Register of Systematic Review (PROSPERO) (CRD42022332760). Results Ten studies were included in this systematic review. A significant value of complete response (CR) ranging from 63–100% in patients with genital warts after receiving several sessions of PDT. A relatively low recurrence rate was seen in all 10 studies, with an RR of less than 17%. Quality assessment of included studies reported mostly high-quality research. Conclusions PDT therapy resulted in a higher CR with significantly lower RR compared to other therapies. Thus, PDT can be an alternative treatment of CA with low RR and minimal side effects. Additional research, especially randomized clinical trials in various countries, is needed to further substantiate this treatment and formulate definitive protocols.
Rehabilitation models of care for children and youth with traumatic brain and/or spinal cord injuries: A focus on service structure, service organization, and the barriers and facilitators of rehabilitation service provision

ABSTRACT To understand the systems underlying current rehabilitation models of care used with children and youth (0–21years) who sustain traumatic brain and/or spinal cord injuries. This study gathered qualitative data on service structures, service organization, and the barriers and facilitators of service provision in selected medical rehabilitation service(s) (MRS) and community-based rehabilitation service(s) (CBRS). Informants from 11 rehabilitation services were interviewed using a semi-structured interview guide. Interviews were analysed in NVivo using content analysis method. Experiences shared by the service representatives indicated that most services supported children and youth with brain injury, with a limited number also specializing in spinal cord injuries. MRS often delivered care in inpatient or outpatient settings, while CBRS offered home/community-based services. Care planning often started either prior to or shortly after admission from acute care settings, using either multidisciplinary or interdisciplinary teamwork models. Strengths of the services included innovation and provision of family-centred care; while challenges experienced included difficulty translating evidence into practice and poor team communication. Models of care were similar across services, with a focus on providing family-centred care. Several shared challenges were described, and service representatives expressed interest in forming partnerships and collaborations to address these challenges through innovative initiatives.
The vortex-shedding process behind two-dimensional bluff bodies

Using a variety of flow-visualization techniques, the flow behind a circular cylinder has been studied. The results obtained have provided a new insight into the vortex-shedding process. Using time-exposure photography of the motion of aluminium particles, a sequence of instantaneous streamline patterns of the flow behind a cylinder has been obtained. These streamline patterns show that during the starting flow the cavity behind the cylinder is closed. However, once the vortex-shedding process begins, this so-called ‘closed’ cavity becomes open, and instantaneous ‘alleyways’ of fluid are formed which penetrate the cavity. In addition, dye experiments also show how layers of dye and hence vorticity are convected into the cavity behind the cylinder, and how they are eventually squeezed out.
Pathogenicity and virulence of African trypanosomes: From laboratory models to clinically relevant hosts

ABSTRACT African trypanosomes are vector-borne protozoa, which cause significant human and animal disease across sub-Saharan Africa, and animal disease across Asia and South America. In humans, infection is caused by variants of Trypanosoma brucei, and is characterized by varying rate of progression to neurological disease, caused by parasites exiting the vasculature and entering the brain. Animal disease is caused by multiple species of trypanosome, primarily T. congolense, T. vivax, and T. brucei. These trypanosomes also infect multiple species of mammalian host, and this complexity of trypanosome and host diversity is reflected in the spectrum of severity of disease in animal trypanosomiasis, ranging from hyperacute infections associated with mortality to long-term chronic infections, and is also a main reason why designing interventions for animal trypanosomiasis is so challenging. In this review, we will provide an overview of the current understanding of trypanosome determinants of infection progression and severity, covering laboratory models of disease, as well as human and livestock disease. We will also highlight gaps in knowledge and capabilities, which represent opportunities to both further our fundamental understanding of how trypanosomes cause disease, as well as facilitating the development of the novel interventions that are so badly needed to reduce the burden of disease caused by these important pathogens.
Demonstrating Parallel Adaptation: How Switching between Two Virtual Bodies with Different Perspectives Enables Dual Motor Adaptation

We demonstrate a dual-motor adaptation over 2 virtual bodies with opposite visuomotor rotation (+ 15° and − 15°). A related study explored the effect of view perspective (1st person view perspective, 1pp, and 3rd person view perspective, 3pp) on a dual motor adaptation behavior. They showed that (1) in 1pp, the adaptation is explicit, while in 3pp, the adaptation is implicit, and (2) the implicit adaptation led to a better dual adaptation. Here we let the participants experiment with explicit and implicit dual motor adaptation by doing a reaching task in 1pp and then in 3pp. We present an ad-hoc motor adaptation score and discuss which adaptation behavior led to a better dual adaptation.
Cutting-Edge Assets for Trust in 5G and Beyond: Requirements, State of the Art, Trends, and Challenges

In 5G and beyond, the figure of cross-operator/domain connections and relationships grows exponentially among stakeholders, resources, and services, with reputation-based trust models being one of the capital technologies leveraged for trustworthy decision-making. This work studies novel 5G assets on which trust can be used to overcome unsuitable decision-making and address current requirements. First, it introduces a background and general architecture of reputation-based trust models. Then, it analyzes pivotal 5G assets on which trust can enhance their performance. In addition, this article performs a comprehensive review of the current reputation models applied to 5G assets and compares their properties, features, techniques, and results. Finally, it provides current trends and future challenges to conducting forthcoming research in the area.