Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial Analysis of Case-Mix and Dialysis Modality Associations

♦ Background: Health-care systems must attempt to provide appropriate, high-quality, and economically sustainable care that meets the needs and choices of patients with end-stage renal disease (ESRD). France offers 9 different modalities of dialysis, each characterized by dialysis technique, the extent of professional assistance, and the treatment site. The aim of this study was 1) to describe the various dialysis modalities in France and the patient characteristics associated with each of them, and 2) to analyze their regional patterns to identify possible unexpected associations between case-mixes and dialysis modalities. ♦ Methods: The clinical characteristics of the 37,421 adult patients treated by dialysis were described according to their treatment modality. Agglomerative hierarchical cluster analysis was used to aggregate the regions into clusters according to their use of these modalities and the characteristics of their patients. ♦ Result: The gradient of patient characteristics was similar from home hemodialyis (HD) to in-center HD and from non-assisted automated peritoneal dialysis (APD) to assisted continuous ambulatory peritoneal dialysis (CAPD). Analyzing their spatial distribution, we found differences in the patient case-mix on dialysis across regions but also differences in the health-care provided for them. The classification of the regions into 6 different clusters allowed us to detect some unexpected associations between case-mixes and treatment modalities. ♦ Conclusions: The 9 modalities of treatment available make it theoretically possible to adapt treatment to patients' clinical characteristics and abilities. However, although we found an overall appropriate association of dialysis modalities to the case-mix, major inter-region heterogeneity and the low rate of peritoneal dialysis (PD) and home HD suggest that factors besides patients' clinical conditions impact the choice of dialysis modality. The French organization should now be evaluated in terms of patients' quality of life, satisfaction, survival, and global efficiency.
The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities

The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.
Characterization of AMPA Receptors Targeted by the Climbing Fiber Transmitter Mediating Presynaptic Inhibition of GABAergic Transmission at Cerebellar Interneuron-Purkinje Cell Synapses

The climbing fiber (CF) neurotransmitter not only excites the postsynaptic Purkinje cell (PC) but also suppresses GABA release from inhibitory interneurons converging onto the same PC depending on AMPA-type glutamate receptor (AMPAR) activation. Although the CF-/AMPAR-mediated inhibition of GABA release provides a likely mechanism boosting the CF input-derived excitation, how the CF transmitter reaches target AMPARs to elicit this action remains unknown. Here, we report that the CF transmitter diffused from its release sites directly targets GluR2/GluR3 AMPARs on interneuron terminals to inhibit GABA release. A weak GluR3-AMPAR agonist, bromohomoibotenic acid, produced excitatory currents in the postsynaptic PCs without presynaptic inhibitory effect on GABAergic transmission. Conversely, a specific inhibitor of the GluR2-lacking/Ca2+-permeable AMPARs, philanthotoxin-433, did not affect the CF-induced inhibition but suppressed AMPAR-mediated currents in Bergmann glia. A low-affinity GluR antagonist, γ-d-glutamylglycine, or retardation of neurotransmitter diffusion by dextran reduced the inhibitory action of CF-stimulation, whereas blockade of glutamate transporters enhanced the CF-induced inhibition. The results suggest that the CF transmitter released after repeated stimulation overwhelms local glutamate uptake and thereby diffuses from the release site to reach GluR2/GluR3 AMPARs on nearby interneuron terminals. Double immunostaining showed that GluR2/3 subunits and glutamate decarboxylase or synaptophysin are colocalized at the perisomatic GABAergic processes surrounding PCs. Finally, electron microscopy detected specific immunoreactivity for GluR2/3 at the presynaptic terminals of symmetric axosomatic synapses on the PC. These findings demonstrate that the CF transmitter directly inhibits GABA release from interneurons to the PC, relying on extrasynaptic diffusion and local heterogeneity in AMPAR subunit compositions.
Anticoagulant therapy for deep vein thrombosis (DVT) in pregnancy.

BACKGROUND Thromboembolic complications are much higher in pregnancy due to procoagulant changes. Heparin does not cross the placenta and the use of unfractionated heparin (UFH) is the current established practice in prophylaxis and treatment for thromboembolism in pregnancy. OBJECTIVES To compare the effectiveness of anticoagulant therapies for the treatment of deep vein thrombosis in pregnancy. The anticoagulant drugs included are UFH, low molecular weight heparin (LMWH) and warfarin. SEARCH STRATEGY We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (March 2010) and reference lists of retrieved studies. SELECTION CRITERIA Randomised controlled trials comparing any combination of warfarin, UFH, LMWH and placebo in pregnant women. DATA COLLECTION AND ANALYSIS We used methods described in the Cochrane Handbooks for Systemic Reviews of Interventions for assessing the eligibility of studies identified by the search strategy. A minimum of two review authors independently assessed each study. MAIN RESULTS We did not identify any eligible studies for inclusion in the review.We identified three potential studies; after assessing eligibility, we excluded all three as they did not meet the prespecified inclusion criteria. One study compared LMWH and UFH in pregnant women with previous thromboembolic events and, for most of these women, anticoagulants were used as thromboprophylaxis. There were only three women who had a thromboembolic event during the current pregnancy and it was unclear whether the anticoagulant was used as therapy or prophylaxis. We excluded one study because it included only women undergoing caesarean birth. The third study was not a randomised trial. AUTHORS' CONCLUSIONS There is no evidence from randomised controlled trials on the effectiveness of anticoagulation for deep vein thrombosis in pregnancy. Further studies are required.
IL-10 Production in Macrophages Is Regulated by a TLR-Driven CREB-Mediated Mechanism That Is Linked to Genes Involved in Cell Metabolism

IL-10 is produced by macrophages in diverse immune settings and is critical in limiting immune-mediated pathology. In helminth infections, macrophages are an important source of IL-10; however, the molecular mechanism underpinning production of IL-10 by these cells is poorly characterized. In this study, bone marrow–derived macrophages exposed to excretory/secretory products released by Schistosoma mansoni cercariae rapidly produce IL-10 as a result of MyD88-mediated activation of MEK/ERK/RSK and p38. The phosphorylation of these kinases was triggered by TLR2 and TLR4 and converged on activation of the transcription factor CREB. Following phosphorylation, CREB is recruited to a novel regulatory element in the Il10 promoter and is also responsible for regulating a network of genes involved in metabolic processes, such as glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation. Moreover, skin-resident tissue macrophages, which encounter S. mansoni excretory/secretory products during infection, are the first monocytes to produce IL-10 in vivo early postinfection with S. mansoni cercariae. The early and rapid release of IL-10 by these cells has the potential to condition the dermal microenvironment encountered by immune cells recruited to this infection site, and we propose a mechanism by which CREB regulates the production of IL-10 by macrophages in the skin, but also has a major effect on their metabolic state.
High-Energy and -Protein Diet Increases Brain and Corticospinal Tract Growth in Term and Preterm Infants After Perinatal Brain Injury

OBJECTIVE. Our hypothesis was that infants with perinatal brain injury fail to thrive in the first postnatal year because of increased energy and protein requirements from deficits that accumulated during neonatal intensive care. Our aim was to assess whether dietary energy and protein input was a rate-limiting factor in brain and body growth in the first year after birth. METHODS. We conducted a prospective, double-blind and randomized, 2-stage group sequential study and controlled for gestation, gender, and brain lesion. Neonates with perinatal brain damage were randomly allocated to receive either a high- (120% recommended average intake) or average (100% recommended average intake) energy and protein diet. The study began at term and continued for 12 months. Three-day dietary diaries estimated energy and protein intake. The primary outcome measure was growth of occipitofrontal circumference. Other measures were growth of axonal diameters in the corticospinal tract, which were estimated by using transcranial magnetic stimulation, weight gain, and length. RESULTS. The study was terminated at the first analysis when the 16 subjects had completed the protocol, because the predetermined stopping criterion of >1 SD difference in occipitofrontal circumference at 12 months’ corrected age in those receiving the higher-energy and -protein diet had been demonstrated. Axonal diameters in the corticospinal tract, length, and weight were also significantly increased. CONCLUSIONS. These data support our hypothesis that infants with significant perinatal brain damage have increased nutritional requirements in the first postnatal year and suggest that decreased postnatal brain growth may exacerbate their impairment. There are no measures of cognitive ability at 12 months of age, and whether there will be any improvement in the status of these children, therefore, remains to be shown.
Increased risk of comorbid rheumatic disorders in vitiligo patients: A nationwide population‐based study

Vitiligo is a common acquired depigmentation disorder. Previous studies have shown that vitiligo is associated with a variety of autoimmune disorders. However, a large‐scale epidemiological study focused on comorbid rheumatic disorders has not been undertaken. To clarify the associations between vitiligo and various rheumatic disorders, we performed a cross‐sectional study using data from the Korean National Health Insurance claims database. Between 2009 and 2013, totals of 86 210 patients with vitiligo and 172 420 age‐ and sex‐matched controls without vitiligo were enrolled in this study. Vitiligo patients were found to be at increased risk of systemic lupus erythematosus, systemic sclerosis, Sjögren's syndrome and rheumatoid arthritis, but no significant association was found between vitiligo and dermatomyositis/polymyositis, Behçet's disease or ankylosing spondylitis. Subgroup analysis showed an increased risk of dermatomyositis/polymyositis in male and ankylosing spondylitis in female vitiligo patients. The risks of dermatomyositis/polymyositis or ankylosing spondylitis were higher in young vitiligo patients. Our study confirms a significant association between vitiligo and rheumatic disorders. Differences in comorbid rheumatic disorders by age group and sex suggest the need for patient‐specific approaches. Careful consideration of rheumatic disorders is required for the proper management of comorbidities in vitiligo patients.
Influence of Cell Differentiation and IL-1β Expression on Clinical Outcomes After Matrix-Associated Chondrocyte Transplantation

Background: Several patient- and defect-specific factors influencing clinical outcomes after matrix-associated chondrocyte transplantation (MACT) have been identified, including the patient’s age, location of the defect, or duration of symptoms before surgery. Little is known, however, about the influence of cell-specific characteristics on clinical results after transplantation. Purpose: The aim of the present study was to investigate the influence of cell differentiation and interleukin-1 β (IL-1β) expression on clinical outcomes up to 5 years after MACT. Study Design: Case series; Level of evidence, 4. Methods: Twenty-seven patients who underwent MACT of the tibiofemoral joint area of the knee were included in this study. Clinical assessments were performed preoperatively as well as 6, 12, 24, and 60 months after transplantation by using the following scores: the Knee injury and Osteoarthritis Outcome Score (KOOS), the International Knee Documentation Committee (IKDC) Subjective Knee Form, the Noyes sports activity rating scale, the Brittberg clinical score, and a visual analog scale (VAS) for pain. The quality of repair tissue was assessed by magnetic resonance imaging using the magnetic resonance observation of cartilage repair tissue (MOCART) score at 1 and 5 years. Cell differentiation (defined as collagen type II:type I expression ratio), aggrecan, and IL-1β expression were determined by real-time polymerase chain reaction in transplant residuals and were correlated with clinical outcomes. Results: The largest improvements in clinical scores were found during the first year. Two years postoperatively, a stable improvement was reached until 5 years after transplantation, with a mean IKDC score of 34.4 ± 8.6 preoperatively to 77.9 ± 16 after 24 months (P < .001). Cell differentiation showed a significant positive correlation with nearly all clinical scores at different time points, especially after 12 months (P < .05). IL-1β expression negatively influenced clinical outcomes at 24 months (Brittberg score) and 60 months (Brittberg and VAS scores) after surgery (P < .05). No correlation was found between the MOCART score and clinical outcomes or gene expression. Conclusion: Our data demonstrate that cell differentiation and IL-1β expression influence clinical outcomes up to 5 years after MACT.
On Self-Dual Cyclic Codes Over Finite Fields

In coding theory, self-dual codes and cyclic codes are important classes of codes which have been extensively studied. The main objects of study in this paper are self-dual cyclic codes over finite fields, i.e., the intersection of these two classes. We show that self-dual cyclic codes of length <i>n</i> over \BBF<i>q</i> exist if and only if <i>n</i> is even and <i>q</i> = 2<i>m</i> with <i>m</i> a positive integer. The enumeration of such codes is also investigated. When <i>n</i> and <i>q</i> are even, there is always a trivial self-dual cyclic code with generator polynomial <i>x</i><sup>n</sup>/<sub>2</sub>+1. We, therefore, classify the existence of self-dual cyclic codes, for given <i>n</i> and <i>q</i> , into two cases: when only the trivial one exists and when two or more such codes exist. Given <i>n</i> and <i>m</i> , an easy criterion to determine which of these two cases occurs is given in terms of the prime factors of <i>n</i>, for most <i>n</i> . We also show that, over a fixed field, the latter case occurs more frequently as the length grows.
THE OCULAR TILT REACTION AND SKEW DEVIATION

The ocular tm reaction composes a triad of ipsilateral head-tilt, ipsilateral conjugate ocular torsion, and skew deviation with Ipsilateral hypotropia It resu~s from a disruption of central vestibular pathways conveying information from the semicircular canals and otoliths. Skew deviation is one component of the syndrome which may or may not be associated with the concomitant torsion and head-tilt of the ocular ! I~ reaction. Because of the frequent clinical presentation of skew deviation it merits special attention. Westheimer and Blair (1975) produced the ocular tilt reaction in monkeys by unilateral electrical stimulation of a region of the brainstem tegmentum dorsolateral to the oculomotor and trochlear nuclei from the caudal wall of the third ventricle to the rostral floor of the fourth ventricle. This area encompasses, but does not consist entirely of, the interstitial nucleus of Cajal. They observed 1) a skew deviation of the eyes resulting from an equal and opposite movement of the globes, 2) a conjugate torsional move­
High-Throughput Screening Assay for Laccase Engineering toward Lignosulfonate Valorization

Lignin valorization is a pending issue for the integrated conversion of lignocellulose in consumer goods. Lignosulfonates (LS) are the main technical lignins commercialized today. However, their molecular weight should be enlarged to meet application requirements as additives or dispersing agents. Oxidation of lignosulfonates with fungal oxidoreductases, such as laccases, can increase the molecular weight of lignosulfonates by the cross-linking of lignin phenols. To advance in this direction, we describe here the development of a high-throughput screening (HTS) assay for the directed evolution of laccases, with lignosulfonate as substrate and the Folin–Ciocalteau reagent (FCR), to detect the decrease in phenolic content produced upon polymerization of lignosulfonate by the enzyme. Once the reaction conditions were adjusted to the 96-well-plate format, the enzyme for validating the assay was selected from a battery of high-redox-potential laccase variants functionally expressed in S. cerevisiae (the preferred host for the directed evolution of fungal oxidoreductases). The colorimetric response (absorbance at 760 nm) correlated with laccase activity secreted by the yeast. The HTS assay was reproducible (coefficient of variation (CV) = 15%) and sensitive enough to detect subtle differences in activity among yeast clones expressing a laccase mutant library obtained by error-prone PCR (epPCR). The method is therefore feasible for screening thousands of clones during the precise engineering of laccases toward valorization of lignosulfonates.
ABF1-binding Sites Promote Efficient Global Genome Nucleotide Excision Repair*

Global genome nucleotide excision repair (GG-NER) removes DNA damage from nontranscribing DNA. In Saccharomyces cerevisiae, the RAD7 and RAD16 genes are specifically required for GG-NER. We have reported that autonomously replicating sequence-binding factor 1 (ABF1) protein forms a stable complex with Rad7 and Rad16 proteins. ABF1 functions in transcription, replication, gene silencing, and NER in yeast. Here we show that binding of ABF1 to its DNA recognition sequence found at multiple genomic locations promotes efficient GG-NER in yeast. Mutation of the I silencer ABF1-binding site at the HMLα locus caused loss of ABF1 binding, which resulted in a domain of reduced GG-NER efficiency on one side of the ABF1-binding site. During GG-NER, nucleosome positioning at this site was not altered, and this correlated with an inability of the GG-NER complex to reposition nucleosomes in vitro.We discuss how the GG-NER complex might facilitate GG-NER while preventing unregulated gene transcription during this process.
In-Cell NMR Characterization of the Secondary Structure Populations of a Disordered Conformation of α-Synuclein within E. coli Cells

α-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson’s disease and related neurodegenerative disorders. We report here the use of in-cell NMR spectroscopy to observe directly the structure and dynamics of this protein within E. coli cells. To improve the accuracy in the measurement of backbone chemical shifts within crowded in-cell NMR spectra, we have developed a deconvolution method to reduce inhomogeneous line broadening within cellular samples. The resulting chemical shift values were then used to evaluate the distribution of secondary structure populations which, in the absence of stable tertiary contacts, are a most effective way to describe the conformational fluctuations of disordered proteins. The results indicate that, at least within the bacterial cytosol, α-synuclein populates a highly dynamic state that, despite the highly crowded environment, has the same characteristics as the disordered monomeric form observed in aqueous solution.
Siglec-G Deficiency Leads to More Severe Collagen-Induced Arthritis and Earlier Onset of Lupus-like Symptoms in MRL/lpr Mice

Siglec-G is a member of the sialic acid–binding Ig-like lectin (Siglec) family expressed on all B cells. Siglec-G–deficient mice show a large expansion of the B1 cell compartment, demonstrating the crucial role of Siglec-G as an inhibitory receptor on this cellular subset. Although Siglec-G–deficient mice did not develop spontaneous autoimmunity, mice double-deficient for Siglec-G and the related Siglec protein CD22 did show autoimmunity at an older age. In this study, we addressed the question of whether loss of Siglec G on its own affects disease severity in animal models of rheumatoid arthritis and systemic lupus erythematosus. Siglec-G–deficient mice showed moderately increased clinical severity and higher inflammation of the knee joints following collagen-induced arthritis, when compared with control mice. The Siglec-G–deficient mouse was also backcrossed to the autoimmune prone MLR/lpr background. Although both Siglec-G–deficient and control MRL/lpr mice developed a lupus-like disease, Siglec-G–deficient MRL/lpr mice showed an earlier occurrence of autoantibodies; a higher lymphoproliferation of B and T cells; and an earlier onset of disease, as shown by proteinuria and glomerular damage in the kidney. Moreover, Siglec-G–deficient female mice showed a significantly reduced survival compared with female control MRL/lpr mice. Thus, the loss of the inhibitory receptor Siglec-G led to a moderate exacerbation of disease severity and early onset in both collagen-induced arthritis and spontaneous lupus nephritis in MRL/lpr mice.
A Best Practice Approach to Community Reentry From Jails for Inmates With Co-Occurring Disorders: The Apic Model

Almost all jail inmates with mental illness will leave correctional settings and return to the community. Inadequate transition planning puts jail inmates who entered the jail in a state of crisis back on the streets in the middle of the same crisis. The outcomes of inadequate transition planning include the compromise of public safety, an increased incidence of psychiatric symptoms, hospitalization, relapse to substance abuse, suicide, homelessness, and rearrest. Although there are no outcomes studies to guide evidence-based transition-planning practices, there is enough guidance from the multisite studies of the organization of jail mental health programs to create a best practice model. This article presents one such model.