Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and Molecular Findings in Osteoporosis-Pseudoglioma Syndrome and the Osteoporosis-Pseudoglioma Collaborative Group

Mutations in the low-density lipoprotein receptor–related protein 5 gene ( LRP5 ) cause autosomal recessive osteo-porosis-pseudoglioma syndrome (OPPG). We sequenced the coding exons of LRP5 in 37 probands suspected of having OPPG on the basis of the co-occurrence of severe congenital or childhood-onset visual impairment with bone fragility or osteoporosis recognized by young adulthood. We found two putative mutant alleles in 26 probands, only one mutant allele in 4 probands, and no mutant alleles in 7 probands. Looking for digenic inheritance, we sequenced the genes encoding the functionally related receptor LRP6, an LRP5 coreceptor FZD4, and an LRP5 ligand, NDP, in the four probands with one mutant allele, and, looking for locus heterogeneity, we sequenced FZD4 and NDP in the seven probands with no mutations, but we found no additional mutations. When we compared clinical features between probands with and without LRP5 mutations, we found no difference in the severity of skeletal disease, prevalence of cognitive impairment, or family history of consanguinity. However, four of the seven probands without detectable mutations had eye pathology that differed from pathology previously described for OPPG. Since many LRP5 mutations are missense changes, to differentiate between a disease-causing mutation and a benign variant, we measured the ability of wild-type and mutant LRP5 to transduce Wnt and Norrin signal ex vivo. Each of the seven OPPG mutations tested, had reduced signal transduction compared with wild-type mutations. These results indicate that early bilateral vitreoretinal eye pathology coupled with skeletal fragility is a strong predictor of LRP5 mutation and that mutations in LRP5 cause OPPG by impairing Wnt and Norrin signal transduction.
Differential expression of the a and retinoic acid receptors in tissues of the rat

We have compared the expression of a and , retinoic acid receptors (RAR-a and RAR-/J) in different rat tissues. The two cDNA probes for RAR-a and RAR-fl each specifically detect two different transcripts. RAR-ax was expressed in all tissues examined, but, in contrast, the expression of RAR-,f was undetectable in some tissues. The data do not support the idea that RAR-fl is specific to epithelial tissues.
An Inﬂection Point of Serum 25-Hydroxyvitamin D for Maximal Suppression of Parathyroid Hormone Is Not Evident from Multi-Site Pooled Data in Children and Adolescents 1,2

In adults, maximal suppression of serum parathyroid hormone (PTH) has commonly been used to determine the sufﬁciency of serum 25-hydroxyvitamin D [25(OH)D]. In children and adolescents, the relationship between serum 25(OH) D and PTH is less clear and most studies reporting a relationship are derived from relatively small samples and homogeneous cohorts. Our objective was to determine the relationship between serum 25(OH)D and PTH in children and adolescents from a large and diverse U.S. cohort and to identify a point of inﬂection of serum 25(OH)D for maximal suppression of serum PTH. Data from 735 participants, ages 7–18 y, were pooled from 3 study sites located in Indiana, Texas, and Massachusetts. A two-phase linear spline was used to model the relationship between serum 25(OH)D and PTH. The value of serum 25(OH)D for maximal suppression of serum PTH was identiﬁed as the inﬂection point of the spline. Before adjustment for site, the inﬂection point of serum 25(OH)D for maximal suppression of serum PTH was 92.4 nmol/L (95% CI: 62.2, 130.7). After adjusting for site, the point of inﬂection was poorly deﬁned and the relationship between serum 25(OH)D and PTH appeared to be linear. The lack of an inﬂection point of serum 25(OH)D for maximal suppression of PTH brings into question the value of using
Practice of Epidemiology Bias Analysis Gone Bad

Quantitative bias analysis comprises the tools used to estimate the direction, magnitude, and uncertainty from systematic errors affecting epidemiologic research. Despite the availability of methods and tools, and guidance for good practices, few reports of epidemiologic research incorporate quantitative estimates of bias impacts. The lack of familiarity with bias analysis allows for the possibility of misuse, which is likely most often unintentional but could occasionally include intentional efforts to mislead. We identified 3 examples of suboptimal bias analysis, one for each common bias. For each, we describe the original research and its bias analysis, compare the bias analysis with good practices, and describe how the bias analysis and research findings might have been improved. We assert no motive to the suboptimal bias analysis by the original authors. Common shortcomings in the examples were lack of a clear bias model, computed example, and computing code; poor selection of the values assigned to the bias model’s parameters; and little effort to understand the range of uncertainty associated with the bias. Until bias analysis becomes more common, community expectations for the presentation, explanation, and interpretation of bias analyses will remain unstable. Attention to good practices should improve quality, avoid errors, and discourage manipulation.
Evolution of yeast mating systems: all roads lead to selfing

Fungi sexually reproduce in heterothallic outcrossing and homothallic selfing modes, and transitions between the two are common throughout the fungal tree of life. A new study in this issue of Current Biology by Krassowski et al [1] reports from the palette of 332 whole genomes for yeast species that the transition from heterothallism to homothallism is common and has repeatedly punctuated the evolutionary trajectory across one of the major lineages of the fungal kingdom. This provides further evidence for pervasive evolutionary forces that promote transitions to selfing modes of sexual reproduction. are self-sterile: sexual sexual.
Estimated Ventricular Size, Asthma Severity, and Exacerbations The Severe Asthma Research Program III Cohort

BACKGROUND: Relative enlargement of the pulmonary artery (PA) on chest CT imaging is associated with respiratory exacerbations in patients with COPD or cystic ﬁ brosis. We sought to determine whether similar ﬁ ndings were present in patients with asthma and whether these ﬁ ndings were explained by differences in ventricular size. METHODS: We measured the PA and aorta diameters in 233 individuals from the Severe Asthma Research Program III cohort. We also estimated right, left, and total epicardial cardiac ventricular volume indices (eERVVI, eELVVI, and eETVVI, respectively). Associations between the cardiac and PA measures (PA-to-aorta [PA/A] ratio, eERVVI-to-eELVVI [eRV/eLV] ratio, eERVVI, eELVVI, eETVVI) and clinical measures of asthma severity were assessed by Pearson correlation, and associations with asthma severity and exacerbation rate were evaluated by multivariable linear and zero-in ﬂ ated negative binomial regression. RESULTS: Asthma severity was associated with smaller ventricular volumes. For example, those with severe asthma had 36.1 mL/m 2 smaller eETVVI than healthy control subjects ( P ¼ .003) and 14.1 mL/m 2 smaller eETVVI than those with mild/moderate disease ( P ¼ .011). Smaller ventricular volumes were also associated with a higher rate of asthma exacerbations, both retrospectively and prospectively. For example, those with an eETVVI less than the median had a 57% higher rate of exacerbations during follow-up than those with eETVVI greater than the median ( P ¼ .020). Neither PA/A nor eRV/eLV was associated with asthma severity or exacerbations. CONCLUSIONS: In patients with asthma, smaller cardiac ventricular size may be associated with more severe disease and a higher rate of asthma exacerbations.
Structural and Biochemical Characterization of the Interaction between KPC-2 β -Lactamase and β -Lactamase Inhibitor Protein,

KPC β -lactamases hydrolyze the “last resort” β -lactam antibiotics (carbapenems) used to treat multi-drug resistant infections, and are compromising efforts to combat life-threatening Gram-negative bacterial infections in hospitals worldwide. Consequently, the development of novel inhibitors is essential for restoring the effectiveness of existing antibiotics. The β -lactamase inhibitor protein (BLIP) is a competitive inhibitor of a number of class A β -lactamases. In this study, we characterize the previously unreported interaction between the KPC-2 β -lactamase and BLIP. Biochemical results show that BLIP is an extremely potent inhibitor of KPC enzymes, binding KPC-2 and KPC-3 with subnanomolar affinity. To understand the basis of affinity and specificity in the β -lactamase/BLIP system, the crystallographic structure of the KPC-2/BLIP complex was solved to 1.9 Å resolution. Computational alanine scanning was also conducted to identify putative hot spots in the KPC-2/BLIP interface. Interestingly, the two complexes making up the KPC-2/BLIP asymmetric unit are distinct, and in one structure the BLIP F142 loop is absent, in contrast to homologous structures where it occupies the active site. This finding and other sources of structural plasticity appear
A highly dense structure boosts energy harvesting and cycling reliabilities of a high-performance lead-free energy harvester

Currently, effective piezoelectric energy harvesters are based on Pb(Zr,Ti)O3 (PZT) ceramics. However, the growing environmental concerns have been pushing the development of viable green alternatives for lead-based piezoelectric ceramics. In this study, a high quality Mn-modified (K0.5Na0.5)NbO3 (Mn-KNN) lead-free piezoelectric ceramic has been prepared, which is promising for use in lead-free piezoelectric energy harvesters. Herein, we showed that the 1.0 mol% Mn-KNN ceramics not only possessed high Curie temperature, but also exhibited excellent energy harvesting performance due to the highly dense fine-grained structure and various domain configurations. In the mode of a cantilever-type energy harvester, a high output power of 85 μW and peak-to-peak voltage of 16 V were obtained at the acceleration of 40 m s−2. Furthermore, the 1.0 mol% Mn-KNN energy harvester exhibits excellent fatigue resistance up to 106 cycles. These findings indicate potential applications of the Mn-KNN piezoelectric energy harvester for self-powered sources of wireless sensor network systems.
The g -subunit rotation and torque generation in F 1 -ATPase from wild-type or uncoupled mutant Escherichia coli

The rotation of the g -subunit has been included in the binding-change mechanism of ATP synthesis y hydrolysis by the proton ATP synthase (F O F 1 ). The Escherichia coli ATP synthase was engineered for rotation studies such that its ATP hydrolysis and synthesis activity is similar to that of wild type. A fluorescently labeled actin filament connected to the g -subunit of the F 1 sector rotated on addition of ATP. This progress enabled us to analyze the g M23K (the g -subunit Met-23 replaced by Lys) mutant, which is defective in energy coupling between catalysis and proton translocation. We found that the F 1 sector produced essentially the same fric- tional torque, regardless of the mutation. These results suggest that the g M23K mutant is defective in the transformation of the mechanical work into proton translocation or vice versa. The ATP synthases (F O
Optimization of High-order Harmonic Generation using an Ultrashort Pulse High-Intensity Laser

High-order harmonic generation is studied mainly in Argon using the Terawatt Laser System in Lund that provides short pulses. After giving an introduction of the setup, the underlying principles of high-order harmonic generation are described. The experiments were done changing a set of parameters and taking a large amount of harmonic spectra. A detailed study of double peaks occurring was made linking them to the short and long trajectories. It is shown that it is possible to choose one of the double peaks by setting the right experimental conditions. Further, a tunability of the harmonics was proved. Towards a higher efficient and more tunable harmonic generation process, the alignment of a parabolic mirror is described.
Intralingual Administration of AAVrh10-miR SOD1 Improves Respiratory But Not Swallowing Function in a Superoxide Dismutase-1 Mouse Model of Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by degeneration of motor neurons and muscles, and death is usually a result of impaired respiratory function due to loss of motor neurons that control upper airway muscles and/or the diaphragm. Currently, no cure for ALS exists and treatments to date do not signiﬁcantly improve respiratory or swallowing function. One cause of ALS is a mutation in the superoxide dismutase-1 ( SOD1 ) gene; thus, reducing expression of the mutated gene may slow the progression of the disease. Our group has been studying the SOD1 G93A transgenic mouse model of ALS that develops progressive respiratory deﬁcits and dysphagia. We hypothesize that solely treating the tongue in SOD1 mice will preserve respiratory and swallowing function, and it will prolong survival. At 6 weeks of age, 11 SOD1 G93A mice (both sexes) received a single intralingual injection of gene therapy (AAVrh10-miR SOD1 ). Another 29 mice (both sexes) were divided into two control groups: (1) 12 SOD1 G93A mice that received a single intralingual vehicle injection (saline); and (2) 17 non-transgenic littermates. Starting at 13 weeks of age, plethysmography (respiratory parameters) at baseline and in response to hypoxia (11% O 2 ) + hypercapnia (7% CO 2 ) were recorded and videoﬂuoroscopic swallow study testing were performed twice monthly until end-stage disease. Minute ventilation during hypoxia + hypercapnia and mean inspiratory ﬂow at baseline were signiﬁcantly reduced ( p < 0.05) in vehicle-injected, but not AAVrh10-miR SOD1 -injected SOD1 G93A mice as compared with wild-type mice. In contrast, swallowing function was unchanged by AAVrh10-miR SOD1 treatment ( p > 0.05). AAVrh10-miR SOD1 injections also signiﬁcantly extended survival in females by * 1 week. In conclusion, this study indicates that intralingual AAVrh10-miR SOD1 treatment preserved respiratory (but not swallowing) function potentially via increasing upper airway patency, and it is worthy of further exploration as a possible therapy to preserve respiratory capacity in ALS patients.
Quantitation of γH2AX Foci in Tissue Samples

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) processes or by exogenous factors, particularly ionizing radiation and radiomimetic compounds. Phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming γH2AX, is an early response to DNA double-strand breaks 1 . This phosphorylation event is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR) 2 . Overall, DSB induction results in the formation of discrete nuclear γH2AX foci which can be easily detected and quantitated by immunofluorescence microscopy 2 . Given the unique specificity and sensitivity of this marker, analysis of γH2AX foci has led to a wide range of applications in biomedical research, particularly in radiation biology and nuclear medicine. The quantitation of γH2AX foci has been most widely investigated in cell culture systems in the context of ionizing radiation-induced DSBs. Apart from cellular radiosensitivity, immunofluorescence based assays have also been used to evaluate the efficacy of radiation-modifying compounds. In addition, γH2AX has been used as a molecular marker to examine the efficacy of various DSB-inducing compounds and is recently being heralded as important marker of ageing and disease, particularly cancer 3 . Further, immunofluorescence-based methods have been adapted to suit detection and quantitation of γH2AX foci ex vivo and in vivo 4,5 . Here, we demonstrate a typical immunofluorescence method for detection and quantitation of γH2AX foci in mouse tissues. is useful for monitoring DSB formation and repair. Apart from its utility in the context of ionizing radiation, the method can be applied to evaluation of the efficacy of DSB-inducing compounds in various tissues, for example the commonly used anticancer anthracyclines such as doxorubicin are known to cause DSBs, and potentially to monitor various pathologies that are characterized by reactive oxygen species-mediated DSBs. Importantly, this protocol is suitable for different mouse tissues.
Sparse and Low-Rank Subspace Data Clustering with Manifold Regularization Learned by Local Linear Embedding

Data clustering is an important research topic in data mining and signal processing communications. In all the data clustering methods, the subspace spectral clustering methods based on self expression model, e.g., the Sparse Subspace Clustering (SSC) and the Low Rank Representation (LRR) methods, have attracted a lot of attention and shown good performance. The key step of SSC and LRR is to construct a proper affinity or similarity matrix of data for spectral clustering. Recently, Laplacian graph constraint was introduced into the basic SSC and LRR and obtained considerable improvement. However, the current graph construction methods do not well exploit and reveal the non-linear properties of the clustering data, which is common for high dimensional data. In this paper, we introduce the classic manifold learning method, the Local Linear Embedding (LLE), to learn the non-linear structure underlying the data and use the learned local geometry of manifold as a regularization for SSC and LRR, which results the proposed LLE-SSC and LLE-LRR clustering methods. Additionally, to solve the complex optimization problem involved in the proposed models, an efficient algorithm is also proposed. We test the proposed data clustering methods on several types of public databases. The experimental results show that our methods outperform typical subspace clustering methods with Laplacian graph constraint.
Assembly & Transport Mechanism of Tripartite Drug Efflux Systems

Summary Multidrug efflux (MDR) pumps remove a variety of compounds from the cell into the external environment. There are five different classes of MDR pumps in bacteria, and quite often a single bacterial species expresses multiple classes of pumps. Although under normal circumstances MDR pumps confer low-level intrinsic resistance to drugs, the presence of drugs and mutations in regulatory genes lead to high level expression of MDR pumps that can pose problems with therapeutic treatments. This review focuses on the resistance nodulation cell division (RND)-class of MDR pumps that assemble from three proteins. Significant recent advancement in structural aspects of the three pump components has shed new light on the mechanism by which the tripartite efflux pumps extrude drugs. This new information will be critical in developing inhibitors against MDR pumps to improve the potency of prescribed drugs.
GFT projection NMR spectroscopy for proteins in the solid state

Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n -step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated ‘sampling problem’ and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins.
Cross-Talk between CLL Cells and Bone Marrow Endothelial Cells: Role of Signal Transducer and Activator of Transcription-3

, Summary Chronic lymphocytic leukemia (CLL) bone marrow is characterized by increased angiogenesis. However, the molecular mediators of neovascularization and the biological significance of increased endothelial cell proliferation in CLL require further investigation. Because signal transducer and activator of transcription (STAT)-3 is constitutively activated in CLL we studied the role of STAT3 in modulating vascular endothelial growth factor (VEGF) expression and the effect of vascular endothelial cells on CLL cells. Using chromatin immunoprecipitation (ChIP) we found that anti-STAT3 antibodies immunoprecipitated DNA of STAT3, VEGF and other STAT3-regulated genes. In addition, STAT3-short interfering RNA significantly reduced mRNA levels of VEGF in CLL cells suggesting that STAT3 induces VEGF expression in CLL. Remarkably, bone marrow CLL cells expressed high levels of VEGF and high VEGF levels were detected in the plasma of patients with untreated CLL and correlated with white blood cell count. CLL bone marrow biopsies revealed increased microvascular density and attachment of CLL cells to endothelial cells. Co-culture of CLL and human umbilical vein endothelial cells (HUVEC) cells showed a similar attachment. Furthermore, co-culture studies with HUVEC showed that HUVEC protected CLL cells from spontaneous apoptosis by direct cell-to-cell contact as assessed by flow cytometry using Annexin V. Our data suggest that constitutively activated STAT3 induces VEGF production by CLL cells and CLL cells derive a survival advantage from endothelial cells via cell-to cell contact. to normal control bone marrow sections (n=9). The blood vessels in bone marrow sections were highlighted by CD34 immunohistochemical staining. We used the Chalkley point overlap morphometric technique (23). Sections stained with anti-CD34 antibodies were scanned at low power (at X40 and X100 magnifications), and then three areas, considered to have the highest vascularity in the section (hotspots), were selected. Then, a 25 point Chalkley eyepiece graticule was applied to each hotspot area at X200 magnification with a Chalkley grid area of 0.1886 mm 2 (Olympus microscope BX41). The dots in the graticule hitting any stained vessel or endothelial cell were counted in each hotspot selected. The highest score of the three hotspot counts was used for analysis. To correct for cellularity, we multiplied the Chalkley counts in the control samples by a factor equal to the difference in cellularity between CLL and control bone marrows. Double antibody staining was conducted by using first VEGF (1:100, RT for 60 minutes; Dako, Carpintera, CA) and Fast-Red substrate (DakoCytomation) as the chromogen. The tissue sections were rewashed in buffer, double-stain block (DakoCytomation) was applied for 3 minutes, and the sections were incubated with the second anti-VEGFR2 antibody, as described above. After the reaction was visualized with diaminobenzidine tetrahydrochloride the tissue sections were then counterstained with hematoxylin.