Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic characteristics of late-night salivary cortisol using liquid chromatography-tandem mass spectrometry.

OBJECTIVE The objective of the study was to describe the diagnostic performance of a commercially available late-night salivary cortisol (NSC) assay using liquid chromatography tandem mass spectrometry. METHODS We retrospectively identified 90 patients who had one or more NSC determinations: 52 patients in whom Cushing syndrome (CS) was excluded or could not be confirmed [group 1 (G1)] and 38 patients in whom CS was confirmed [group 2 (G2)]. Eighteen healthy volunteers served as controls. RESULTS Baseline demographics in all groups were similar with regards to age, ethnicity, gender, and body mass index. NSC levels [median (range)] were higher in G2, 381 (64-13,500) ng/dl [10.51 (1.77-372.46) nmol/liter], compared with controls, 19.3 (2.1-416) ng/dl [0.53 (0.06-11.48) nmol/liter], and G1, 26 (4-176) ng/dl [0.72 (0.11-4.86) nmol/liter, P < 0.001]. The highest combined sensitivity (92%) and specificity (92%) was achieved at a cut point of 107 ng/dl (2.95 nmol/liter). Two or more NSCs were done in 32 of 52 G1 and 31 of 38 G2 patients. In G1 eight of 32 (25%) had at least one elevated [>100 ng/dl (2.76 nmol/liter)] NSC including two in whom both NSCs were elevated. In contrast, four of 31 (13%) in G2 had at least one normal NSC including one with four of five normal NSC values. None of the patients with CS had a NSC less than 60 ng/dl (<1.66 nmol/liter). Comparing G1 and G2, obtaining more than one saliva sample did not improve the diagnostic accuracy of NSC measurement (P = 0.64). CONCLUSION The liquid chromatography tandem mass spectrometry assay to measure NSC is a simple and reliable test to screen patients suspected to have CS. Clinicians should be aware of appropriate cutoff values for proper interpretation of NSC and use additional tests when necessary.
Un Plesiosaurio nuevo del Cretáceo del Chubut

A mediados del mes de septiembre del ano pasado, el doctor Pablo Groeber tuvo la gentileza de enviar al Departamento de Paleozoologia, Vertebrados, de nuestro Museo, en nombre de la Direccion de Minas y Geologia del Ministerio de Agricultura de la Nacion, y en concepto de donacion, algunos restos de un reptil fosil de gran tamano obtenidos en el Cretaceo superior del noroeste del Chubut por el senor Cristian S. Petersen, con la cooperacion del poblador de aquella zona Victor Saldivia. Vinieron dichos restos cubiertos de una dura capa de roca, y al ser limpiados y preparados cuidadosamente por el preparador senor Parodi, se vio, con la sorpresa y satisfaccion consiguientes, que se trataba de un enorme sauropterigio del suborden Plesiosauria. Poco tiempo antes, al regreso de una excursion al cerro Mirador, en la misma region, el director del Museo, doctor Joaquin Frenguelli, habia traido como obsequio del senor Mario Reguilo una vertebra incompleta y tres falanges que sin duda corresponden a la misma especie, pero lo fragmentario de este material y la incertidumbre sobre su procedencia exacta no consintieron aventurar su determinacion taxonomica. De informaciones posteriores sin embargo, parece deducirse que estos restos pertenecen al mismo esqueleto que los recibidos por intermedio del doctor Groeber. Sin dificultad se comprendera el considerable interes que tienen estos hallazgos si se tiene en cuenta que, pese a la polvareda levantada hace diez y ocho anos en torno a las absurdas noticias sobre la supuesta existencia de un plesiosaurio vivo en Patagonia, en realidad es esta la primera vez que de un modo absolutamente seguro se puede afirmar que esta clase de reptiles ha vivido en lo que hoy es territorio argentino.
Individual left‐hand and right‐hand intra‐digit representations in human primary somatosensory cortex

Individual intra‐digit somatotopy of all phalanges of the middle and little finger of the right and left hand was studied by functional magnetic resonance imaging in 12 healthy subjects. Phalanges were tactilely stimulated and activation in BA 3b of the human primary somatosensory cortex could be observed for each individual phalanx. Activation peaks were further analysed using the Direction/Order (DiOr) method, which identifies somatotopy, if a significantly high number of subjects exhibit ordered distal‐to‐proximal phalanx representions along a similar direction. Based on DiOr, ordered and similar‐direction‐aligned intra‐digit maps across subjects were found at the left hand for the little and middle finger and at the right hand for the little finger. In these digits the proximal phalanges were represented more medially along the course of the central sulcus than the distal phalanges. This is contrasted by the intra‐digit maps for the middle finger of the right hand, which showed larger inter‐subject variations of phalanx alignments without a similar within‐digit representation across subjects. As all subjects were right‐handed and as the middle finger of the dominant hand probably plays a more individual role in everyday tactile performance than the little finger of the right hand and all left‐hand digits, the observed variation might reflect a functional somatotopy based on individual use of that particular digit at the dominant hand.
Composing the L2-M2 Self: A Grounded Theory Study on the Concerns of Adult Irish Sign Language Learners

ed primary data. The array of literature which was consulted during this process is primarily related to the psychology of the language learner and the performance of language. The main concern of this substantive population is EXPOSURE INSECURITY. This is associated with the learner’s perception that they are being intently observed when performing ISL and feel exposed due to the physicality of using the body to express this language. In essence, there is NOWHERE TO HIDE in this context. It is a phenomenon which they have not experienced to the same degree when performing spoken language. The theory of COMPOSING THE L2-M2 SELF captures a two-pronged process; maintaining composure when dealing with the main concern of EXPOSURE INSECURITY and the composing of A PIECE, i.e. the performative aspect associated with producing a signed language. This conceptual account explores how learners develop the resources to be able to tackle their main concern as they progress through the learning journey.
IGFs and IGF-binding proteins in short children with steroid-dependent nephrotic syndrome on chronic glucocorticoids: changes with 1 year exogenous GH.

OBJECTIVE Children with steroid-dependent nephrotic syndrome (SDNS), despite being in remission on glucocorticoids, continue to have growth retardation and short stature. The mechanism is uncertain as both chronic glucocorticosteroids and the nephrotic syndrome may independently affect growth. We investigated the changes in the IGFs and IGF-binding proteins (IGFBPs) in a group of short SDNS children, and studied the changes prospectively with 1 year's treatment with GH. DESIGN AND METHODS Total and 'free' IGF-I, IGFBP-3 and acid-labile subunit (ALS) were studied in eight SDNS boys (mean age=12.6 years; mean bone age=9.1 years) on long term oral prednisolone (mean dose 0.46 mg/kg per day) before, during, and after, 1 year's treatment with GH (mean dose 0.32 mg/kg per week). Pretreatment comparisons were made with two control groups, one matched for bone age (CBA; mean bone age=9.2 years), and another for chronological age (CCA; mean chronological age=13 years). Subsequently, three monthly measurements of serum and urine IGFBPs were carried out in the GH-treated SDNS patients using Western ligand blot and Western immunoblot. RESULTS Pre-treatment serum total IGF-I levels and the IGF-I/IGFBP-3 ratio were elevated significantly in SDNS compared with CBA, and were similar to CCA. Serum free IGF-I levels were elevated significantly compared with both control groups, but serum IGFBP-3 did not differ significantly. Urinary IGFBP-2, IGFBP-3 and ALS were detectable in the SDNS children only. With GH treatment, IGF-I and IGFBP-3, but not IGF-II, increased significantly compared with pre-treatment values, and returned to baseline after cessation of GH treatment. Urinary IGFBPs did not change significantly with GH treatment. CONCLUSIONS There is persistent urinary loss of IGFBP-2, IGFBP-3 and ALS in children with SDNS in remission with growth retardation. However, the significant elevation in serum IGF-I suggests that glucocorticoid-induced resistance to IGF is the main factor responsible for the persistent growth retardation in these children. Exogenous GH was able to overcome this resistance by further increasing serum IGF-I.
Nutraceutical Therapies for Degenerative Joint Diseases: A Critical Review

There is growing recognition of the importance of nutritional factors in the maintenance of bone and joint health, and that nutritional imbalance combined with endocrine abnormalities may be involved in the pathogenesis of osteoarthritis (OA) and osteochondritis dissecans (OCD). Despite this, dietary programs have played a secondary role in the management of these connective tissue disorders. Articular cartilage is critically dependent upon the regular provision of nutrients (glucose and amino acids), vitamins (particularly vitamin C), and essential trace elements (zinc, magnesium, and copper). Therefore, dietary supplementation programs and nutraceuticals used in conjunction with non-steroidal, anti-inflammatory drugs (NSAIDs) may offer significant benefits to patients with joint disorders, such as OA and OCD. This article examines the available clinical evidence for the efficacy of nutraceuticals, antioxidant vitamin C, polyphenols, essential fatty acids, and mineral cofactors in the treatment of OA and related joint disorders in humans and veterinary species. This article also attempts to clarify the current state of knowledge. It also highlights the need for additional targeted research to elucidate the changes in nutritional status and potential alterations to the expression of plasma membrane transport systems in synovial structures in pathophysiological states, so that current therapy and future treatments may be better focused.
Are protein–protein interfaces more conserved in sequence than the rest of the protein surface?

Protein interfaces are thought to be distinguishable from the rest of the protein surface by their greater degree of residue conservation. We test the validity of this approach on an expanded set of 64 protein–protein interfaces using conservation scores derived from two multiple sequence alignment types, one of close homologs/orthologs and one of diverse homologs/paralogs. Overall, we find that the interface is slightly more conserved than the rest of the protein surface when using either alignment type, with alignments of diverse homologs showing marginally better discrimination. However, using a novel surface‐patch definition, we find that the interface is rarely significantly more conserved than other surface patches when using either alignment type. When an interface is among the most conserved surface patches, it tends to be part of an enzyme active site. The most conserved surface patch overlaps with 39% (± 28%) and 36% (± 28%) of the actual interface for diverse and close homologs, respectively. Contrary to results obtained from smaller data sets, this work indicates that residue conservation is rarely sufficient for complete and accurate prediction of protein interfaces. Finally, we find that obligate interfaces differ from transient interfaces in that the former have significantly fewer alignment gaps at the interface than the rest of the protein surface, as well as having buried interface residues that are more conserved than partially buried interface residues.
Mechanisms of HIV Transmission in Depo-Provera Users: The Likely Role of Hypoestrogenism

Almost half of new HIV infections worldwide occur in women, and vaginal intercourse is the most common mode of transmission. Accumulating evidence suggests that depot medroxyprogesterone acetate may increase HIV transmission, but little is known about the underlying mechanisms. We propose that hypoestrogenism in depot medroxyprogesterone acetate may contribute to increased HIV transmission. We present supportive evidence and propose potential interventions to prevent or treat vaginal hypoestrogenism using vaginal estrogens.
Aligning Short Sequencing Reads with Bowtie

This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools. Curr. Protoc. Bioinform. 32:11.7. 1‐11.7. 14. © 2010 by John Wiley & Sons, Inc.
Management of post-intubation tracheal stenoses using the endoscopic approach.

BACKGROUND AND AIM Tracheal stenosis is a common complication of intubation with or without subsequent tracheotomy whose management remains poorly defined. Over 600 post-intubation tracheal stenoses have been treated in our centre since 1982: the aim of this study was to determine the safety and efficacy of our endoscopic approach. METHODS This retrospective study includes 113 new cases treated between 1998 and 2001. We chose this period to have a standardised technique and a significant number of cases with a sufficiently long follow up (28-78 months). Forty patients who did not meet the criteria for "true stenosis" (granulomas, pseudoglottic stenosis, etc.) were excluded from the study. RESULTS 73 patients (50+/-21 years) entered the study: 13 (18%) web-like and 60 (82%) complex stenoses. Most web-like stenoses were successfully treated with Laser Assisted Mechanical Dilation (LAMD) alone; among complex stenoses LAMD was sufficient to treat 13 patients (22%), whereas 47 patients (78%) required stent placement: 22 had their stent removed after one year and did not require any further therapy, 13 inoperable patients required permanent stent and 12 were referred to surgery after failure of multiple endoscopic treatments. No permanent complications secondary to endoscopic treatment were observed. 48 patients (66%) obtained a stable, good result with the endoscopic procedure, 13 (18%) required a permanent stent while 12 patients (16%) were referred to surgery. CONCLUSIONS Our results indicate that the endoscopic treatment of post-intubation tracheal stenoses performed in an expert setting can be considered a safe first-line therapy, leaving some selected cases and the relapsing stenoses, for surgical resection.
Further antigenic characterization of porcine rotavirus YM

We recently reported that the serotype specificity of YM, a group A porcine rotavirus, is different from those of the previously established rotavirus serotypes, 1 to 6 (A. M. Ruiz, I. V. Lopez, S. Lopez, R. T. Espejo, and C. F. Arias, J. Virol. 62:4331-4336, 1988). Here we demonstrate by cross-neutralization studies that rotavirus YM is also antigenically distinct from prototype rotavirus strains of serotypes 7 (Ty1), 8 (69M), 9 (WI61), and 10 (B223). A comparison of the serotype-determining amino acid regions of the YM surface glycoprotein, VP7, with the reported homologous sequences of rotavirus strains Gottfried, 69M, B37, F45, and WI61 further supported the serotypic individuality of the rotavirus YM VP7 protein.
SOCIETY STRUCTURE AND VIOLENCE AGAINST WOMEN

ڃليلپ ذځڈْف هك ڄاٴ ذٍا يځبچع ڇ يقيهبر يا ټڅ ح ڇ ٤ٽاڈع هاڇكا ٻبپر ذٍا ڄزّاك كڈعڇ . ڄڅك ىا ڃليلپ ڀيا ڄث ڄعڈر 70 لّ ىب٩آ يكلايٽ ِڅڇژپ ڇ ٻبغځا ڃىڈؽ ڀيا هك يكل٦زٽ يبڅ ذ٭وگ . يٍهوث ةبث هك ڃاوپڅ يرلاوٴْٽ بث ذځڈْف ذٍا . ِڅڇژپ ڀيا هك ىڈؽ كهاڇ ٰٲؾٽ بڅ ح يٕڈٖف ڃكاڈځبف يپيپٕ ڇ يٽ كڈّ هك ڇ ٓڈٖف يهبز٭ه يٽ ۇٴاڈئٍ كاو٭ا ىا ًبَؽ لڂاٴ . هك ذځڈْف كڈعڇ ڄث يځبثوٱ ٫وٝ ىا ڃكاڈځبف يٴٺ٥ ٿبچڂپ ٬ٺزقٽ يٽ ڄزّاك ڃبگځ يٽ ُڈٽاو٭ ،كڈّ هك بي ڇ كڈّ يٽ ٯاو٩ا ٿآ ٿبيث كڈّ . هك هبٽآ كڈجځ ٓڈٖف كاو٭ا ٗو٦ٽ هك ذځڈْف ، هك يوگيك يٴوٴْٽ ڃاه ذٍك بي ٿڈپځ ڄث يث ح ذٍا ٫و٦ٽ . ڄاٴ يوگيك يٴوٴْٽ يٍهوث هك يٽ ڃلڅبْٽ ذځڈْف يبڅ تر كڈّ ي ڀي يبڅ كڈعڈٽ يو٢ځ ذٍا . ڃبگليك ىا يهبيَث يو٢ځ يبڅ ٻ يٴٽاڈ٥ كڈعڈٽ ؤ ؼٍٞ هك اه ذځڈْف ىڇوث هك وص يگژيڇ يبڅ « يكو٭ لڂځبٽ » ؼٍٞ هك بي ڇ « يگكاڈځبف لڂځبٽ » يٽ و٢ځ هك لځويگ . ڀيا ڄيٺاٴ ٓ ذفبڂّ هك يٴٽاڈ٥ د ڃليلپ ىا ؼيؽ أ ويص لځهاك . ڄيو٢ځ يجر ذَيڂيپ٭ ٿاىاكوپ ي ٿ بي يكو٭ يبڅ
The role of antibody to human beta4 integrin in conjunctival basement membrane separation: possible in vitro model for ocular cicatricial pemphigoid.

PURPOSE To demonstrate the specific binding of autoantibodies present in the sera of patients with ocular cicatricial pemphigoid (OCP) to human beta4 integrin present in the normal human conjunctiva (NHC) and to study the role of OCP autoantibodies and antibody to human beta4 integrin in the pathogenesis of subepithelial lesion formation in OCP. METHODS Indirect immunofluorescence assay and in vitro organ culture method using NHC were used. Sera and IgG fractions from 10 patients with OCP; immunoaffinity-purified OCP autoantibody; antibodies to human beta4, beta1, alpha6, and alpha5 integrins; and sera from patients with pemphigus vulgaris, bullous pemphigoid (BP), and chronic atopic and chronic ocular rosacea cicatrizing conjunctivitis; and normal human serum (NHS) were used. RESULTS Nine of 10 OCP sera or IgG fractions, immunoaffinity-purified OCP autoantibody, antibodies to human beta4 and alpha6 integrins, and sera from patients with BP showed homogenous, smooth linear binding along the basement membrane zone (BMZ) of the NHC. NHS, antibodies to other integrins, and sera from patients with chronic cicatrizing conjunctivitis from other causes showed no such binding. When NHC was first absorbed with OCP sera and then reacted with anti-beta4 antibodies or vice versa, the intensity of the BMZ binding was dramatically reduced or completely eliminated, indicating that there were autoantibodies in OCP sera specific for the beta4 integrin. BMZ separation developed 48 to 72 hours after addition of total OCP sera, IgG fractions from OCP sera, immunoaffinity-purified autoantibodies from sera of patients with OCP, or anti-beta4 antibodies to the NHC cultures, but not after addition of normal control sera, sera from patients with chronic cicatrizing conjunctivitis from causes other than OCP, or sera from patients with OCP in clinical remission. CONCLUSION Circulating anti-beta4 integrin antibody may have an important role in the pathogenesis of OCP.
Anatomical features associated with water transport in imperforate tracheary elements of vessel-bearing angiosperms.

BACKGROUND AND AIMS Imperforate tracheary elements (ITEs) in wood of vessel-bearing angiosperms may or may not transport water. Despite the significance of hydraulic transport for defining ITE types, the combination of cell structure with water transport visualization in planta has received little attention. This study provides a quantitative analysis of structural features associated with the conductive vs. non-conductive nature of ITEs. METHODS Visualization of water transport was studied in 15 angiosperm species by dye injection and cryo-scanning electron microscopy. Structural features of ITEs were examined using light and electron microscopy. KEY RESULTS ITEs connected to each other by pit pairs with complete pit membranes contributed to water transport, while cells showing pit membranes with perforations up to 2 µm were hydraulically not functional. A close relationship was found between pit diameter and pit density, with both characters significantly higher in conductive than in non-conductive cells. In species with both conductive and non-conductive ITEs, a larger diameter was characteristic of the conductive cells. Water transport showed no apparent relationship with the length of ITEs and vessel grouping. CONCLUSIONS The structure and density of pits between ITEs represent the main anatomical characters determining water transport. The pit membrane structure of ITEs provides a reliable, but practically challenging, criterion to determine their conductive status. It is suggested that the term tracheids should strictly be used for conductive ITEs, while fibre-tracheids and libriform fibres are non-conductive.
Optical Coherence Tomography Study of Retinal and Choroidal Changes in Patients with Chronic Obstructive Pulmonary Disease

Background: Chronic obstructive pulmonary disease (COPD) has multi-systemic implications and comorbidities. Fine ocular structures are affected by hypoxia and systemic inflammation. Objective: To evaluate the changes in the retina and choroid in patients with chronic obstructive pulmonary disease using spectral-domain optical coherence tomography (SD-OCT). Patients and methods: This prospective case control study included a total of forty COPD patients and twenty ageand sex-matched healthy individuals as control group; both eyes were included. COPD patients were divided into two subgroups; a group with mild to moderate COPD and another group with severe to very severe COPD according to the Global Initiative for COPD guideline. COPD patients were subjected to spirometry. Arterial blood gas analysis was performed to determine hypoxic state. The subfoveal choroidal thickness (SFCT), macular thickness (MT) and retinal nerve fiber layer (RNFL) thickness were measured using SD-OCT and compared between groups. Results: There was no statistically significant difference between groups according to demographic data. Mean SFCT was statistically significantly thinner in COPD groupsthan in the control group; and this thinning was more pronounced with increase in the severity of COPD. As regard to MT, no statistically significant difference was observed between groups (p=0.691). Peripapillary RNFL was significantly thinner in COPD group than the control group in all quadrants except the superior one. Conclusion: Changes in the SFCT and RNFL thickness could be used as indicators for the severity of COPD
EMR4, a Novel Epidermal Growth Factor (EGF)-TM7 Molecule Up-regulated in Activated Mouse Macrophages, Binds to a Putative Cellular Ligand on B Lymphoma Cell Line A20*

A novel member of the EGF-TM7 family, mEMR4, was identified and characterized. The full-length mouse EMR4 cDNA encodes a predicted 689-amino acid protein containing two epidermal growth factor (EGF)-like modules, a mucin-like spacer domain, and a seven-transmembrane domain with a cytoplasmic tail. Genetic mapping established thatmEMR4 is localized in the distal region of mouse chromosome 17 in close proximity to another EGF-TM7 gene,F4/80 (Emr1). Similar toF4/80, mEMR4 is predominantly expressed on resident macrophages. However, a much lower expression level was also detected in thioglycollate-elicited peritoneal neutrophils and bone marrow-derived dendritic cells. The expression ofmEMR4 is up-regulated following macrophage activation in Biogel and thioglycollate-elicited peritoneal macrophages. Similarly, mEMR4 is over-expressed in TNF-α-treated resident peritoneal macrophages, whereas interleukin-4 and -10 dramatically reduce the expression. mEMR4 was found to undergo proteolytic processing within the extracellular stalk region resulting in two protein subunits associated noncovalently as a heterodimer. The proteolytic cleavage site was identified by N-terminal amino acid sequencing and located at the conserved GPCR (G protein-coupled receptor) proteolytic site in the extracellular region. Using multivalent biotinylated mEMR4-mFc fusion proteins as a probe, a putative cell surface ligand was identified on a B lymphoma cell line, A20, in a cell-binding assay. The mEMR4-ligand interaction is Ca2+-independent and is mediated predominantly by the second EGF-like module. mEMR4 is the first EGF-TM7 receptor known to mediate the cellular interaction between myeloid cells and B cells.