Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Postoperative Subcutaneous Tissue Oxygen Predicts Surgical Site Infection

BACKGROUND:Subcutaneous oxygen partial pressure is one of several determinants of surgical site infections (SSIs). However, tissue partial pressure is difficult to measure and requires invasive techniques. We tested the hypothesis that early postoperative tissue oxygen saturation (StO2) measured with near-infrared spectroscopy predicts SSI. METHODS:We evaluated StO2 in 116 patients undergoing elective colon resection. Saturation was measured near the surgical incision, at the upper arm, and at the thenar muscle with an InSpectra™ tissue spectrometer model 650 (Hutchinson Technology Inc., Hutchinson, MN) 75 minutes after the end of surgery and on the first postoperative day. An investigator blinded to StO2 assessed patients daily for wound infection. Receiver operating characteristic curves were used to analyze the performance of StO2 measurements as a predictor of SSI. RESULTS:In 23 patients (≈20%), SSI was diagnosed 9 ± 5 days (mean ± SD) after surgery. Patients who did and did not develop an SSI had similar age (48 ± 14 vs 48 ± 15 years, respectively; P = 0.97) and gender (female:male, 15:8 vs 46:47, respectively), but patients who developed SSI weighed more (body mass index 32 ± 7 vs 27 ± 6 kg/m2; P < 0.01). StO2 at the upper arm was lower in patients who developed SSI than in those who did not develop SSI (52 ± 22 vs 66 ± 21; P = 0.033), and these measurements had a sensitivity of 71% and specificity of 60% for predicting SSI, using StO2 of 66% as the cutoff point. CONCLUSION:StO2 measured at the upper arm only 75 minutes after colorectal surgery predicted development of postoperative SSI, although the infections were typically diagnosed more than a week later. Although further testing is required, StO2 measurements may be able to predict SSI and thus allow earlier preventive measures to be implemented.
Lidocaine patch 5% and its positive impact on pain qualities in osteoarthritis: results of a pilot 2-week, open-label study using the Neuropathic Pain Scale

SUMMARY Objective: To determine the impact of the lidocaine patch 5% on distinct pain qualities associated with osteoarthritis (OA) through use of the Neuropathic Pain Scale (NPS), an assessment tool designed to assess intensity of various pain qualities (i.e. sharp, dull). Patients and methods: Patients were enrolled in a prospective, open-label, non-randomized, parallel-group, 2-week study involving 8 clinical trial sites in the United States. Eligible patients had radiographic evidence of OA involving one or both knees and reported moderate-to-severe pain (despite prn or stable doses of analgesics) on the NPS at study enrollment. Patients on prn analgesics were discontinued from all analgesic regimens prior to study entry and received lidocaine patch 5% as monotherapy. Those on stable doses of analgesics were continued on their other analgesic regimens with no additions or dose alterations allowed other than the lidocaine patch 5% as add-on therapy. The lidocaine patch 5% was applied to the area of maximal pain, using no more than a total of 4 patches changed every 24 h. Effectiveness was measured by change from baseline to Week 2 in 4 composite measures of the NPS: NPS-10, NPS-4, NPS-8, and NPS-non-allodynia. Safety was assessed by adverse events (AEs), dermal assessment of application site(s), and skin sensory testing. Results: In the combined patient population (n = 100), 2 weeks of treatment with lidocaine patch 5% significantly improved all 4 NPS composite measures ( p < 0.001). Separate analyses by subgroups revealed significant improvements in all 4 composite measures for both the monotherapy group (n = 12; p < 0.01) and add-on therapy group (n = 88; p < 0.001). No treatment-related AEs were reported for the monotherapy group. In the add-on therapy group, 5 patients experienced mild-to-moderate treatment-related AEs. Conclusions: In patients with moderate-to-severe OA of the knee, 2 weeks of treatment with the lidocaine patch 5% significantly reduces the intensity of pain qualities as measured by all 4 NPS composite measures. Our results coincide with previously reported improvements in pain and physical function in the same patient population, as measured by the Western Ontario and McMaster Universities OA Index. Measuring the various qualities of pain appears to be a valid approach for assessing clinical outcomes in the treatment of OA pain. Pain measures such as the NPS can capture the multi-dimensional properties of a patient's pain experience and may offer clinicians the possibility to identify differential effects of analgesic treatments on various pain qualities associated with OA.
Front-line treatment of advanced non-small-cell lung cancer with docetaxel and gemcitabine: a multicenter phase II trial.

PURPOSE To evaluate the tolerance and efficacy of the combination of docetaxel and gemcitabine in patients with advanced non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS Fifty-one chemotherapy-naive patients with NSCLC were treated with gemcitabine 900 mg/m2 intravenously on days 1 and 8 and docetaxel 100 mg/m2 intravenously on day 8 with granulocyte colony-stimulating factor (150 microg/m2, subcutaneously) support from day 9 to day 15. Treatment was repeated every 3 weeks. RESULTS The patients' median age was 64 years. The World Health Organization performance status was 0 to 1 in 39 patients and 2 in 12 patients. Fifteen patients (29%) had stage IIIB disease, and 36 (71%) had stage IV; histology was mainly squamous cell carcinoma (59%). A partial response was achieved in 19 patients (37.5%; 95% confidence interval, 24% to 50%); stable disease and progressive disease were each observed in 16 patients (31.4%). The median duration of response and the time to tumor progression were 5 and 6 months, respectively. The median survival was 13 months, and the actuarial 1-year survival was 50.7%. Grade 4 anemia and thrombocytopenia were rare (2%). Four patients (8%) developed grade 3 or 4 neutropenia, and all were complicated with fever; there was no treatment-related death. Grade 3 or 4 diarrhea occurred in three patients (6%), grade 2 or 3 neurotoxicity in four patients (8%), grade 2 or 3 asthenia in 10 patients (20%), and grade 2 or 3 edema in 10 patients (20%). CONCLUSION The combination of docetaxel/gemcitabine is well tolerated, can be used for outpatients, and is active for the treatment of advanced NSCLC. This treatment merits further comparison with other cisplatin- or carboplatin-based combinations.
DCT based algorithm for blurred regions determination in digital images

One of the common irregularities in digital images is blur, which is usually caused by the object motion, camera shake or out of focus. In this paper we present an algorithm for detecting images with blur, or blurred regions within an image. Blur is detected by analyzing DCT coefficients and introducing function and threshold for classification of appropriately sized sub-regions as blurred or non-blurred. Additionally, algorithm has a component for blur detection on pixel level. Our proposed algorithm exhibited superior performance compared to one of DCT based algorithms from literature.
SIP1, a Novel Zinc Finger/Homeodomain Repressor, Interacts with Smad Proteins and Binds to 5′-CACCT Sequences in Candidate Target Genes*

Activation of transforming growth factor β receptors causes the phosphorylation and nuclear translocation of Smad proteins, which then participate in the regulation of expression of target genes. We describe a novel Smad-interacting protein, SIP1, which was identified using the yeast two-hybrid system. Although SIP1 interacts with the MH2 domain of receptor-regulated Smads in yeast andin vitro, its interaction with full-length Smads in mammalian cells requires receptor-mediated Smad activation. SIP1 is a new member of the δEF1/Zfh-1 family of two-handed zinc finger/homeodomain proteins. Like δEF1, SIP1 binds to 5′-CACCT sequences in different promoters, including the Xenopus brachyury promoter. Overexpression of either full-length SIP1 or its C-terminal zinc finger cluster, which bind to the Xbra2promoter in vitro, prevented expression of the endogenousXbra gene in early Xenopus embryos. Therefore, SIP1, like δEF1, is likely to be a transcriptional repressor, which may be involved in the regulation of at least one immediate response gene for activin-dependent signal transduction pathways. The identification of this Smad-interacting protein opens new routes to investigate the mechanisms by which transforming growth factor β members exert their effects on expression of target genes in responsive cells and in the vertebrate embryo.
Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins

The amino acid sequences of soluble, ordered proteins with stable structures have evolved due to biological and physical requirements, thus distinguishing them from random sequences. Previous analyses have focused on extracting the features that frequently appear in protein substructures, such as α‐helix and β‐sheet, but the universal features of protein sequences have not been addressed. To clarify the differences between native protein sequences and random sequences, we analyzed 7368 soluble, ordered protein sequences, by inspecting the observed and expected occurrences of 400 amino acid pairs in local proximity, up to 10 residues along the sequence in comparison with their expected occurrence in random sequence. We found the trend that the hydrophobic residue pairs and the polar residue pairs are significantly decreased, whereas the pairs between a hydrophobic residue and a polar residue are increased. This trend was universally observed regardless of the secondary structure content but was not observed in protein sequences that include intrinsically disordered regions, indicating that it can be a general rule of protein foldability. The possible benefits of this rule are discussed from the viewpoints of protein aggregation and disorder, which are both caused by low‐complexity regions of hydrophobic or polar residues.
Medicago LYK3, an Entry Receptor in Rhizobial Nodulation Factor Signaling1[W]

Rhizobia secrete nodulation (Nod) factors, which set in motion the formation of nitrogen-fixing root nodules on legume host plants. Nod factors induce several cellular responses in root hair cells within minutes, but also are essential for the formation of infection threads by which rhizobia enter the root. Based on studies using bacterial mutants, a two-receptor model was proposed, a signaling receptor that induces early responses with low requirements toward Nod factor structure and an entry receptor that controls infection with more stringent demands. Recently, putative Nod factor receptors were shown to be LysM domain receptor kinases. However, mutants in these receptors, in both Lotus japonicus (nfr1 and nfr5) and Medicago truncatula (Medicago; nfp), do not support the two-receptor model because they lack all Nod factor-induced responses. LYK3, the putative Medicago ortholog of NFR1, has only been studied by RNA interference, showing a role in infection thread formation. Medicago hair curling (hcl) mutants are unable to form curled root hairs, a step preceding infection thread formation. We identified the weak hcl-4 allele that is blocked during infection thread growth. We show that HCL encodes LYK3 and, thus, that this receptor, besides infection, also controls root hair curling. By using rhizobial mutants, we also show that HCL controls infection thread formation in a Nod factor structure-dependent manner. Therefore, LYK3 functions as the proposed entry receptor, specifically controlling infection. Finally, we show that LYK3, which regulates a subset of Nod factor-induced genes, is not required for the induction of NODULE INCEPTION.
CD21 augments antigen presentation in immune individuals

CD21 (complement receptor 2, CR2) binds the C3 degradation products, iC3b and C3d, which are covalently linked to antigen or immune complexes in the process of complement activation. The ability of antigen‐nonspecific B cells to present immune complexes containing high titers of acquired antibodies was tested. Influenza virus was incubated with serum from immune donors to create complement‐containing complexes. These bound specifically to CD21 on transfected fibroblasts and B cell lines, as measured by microcytofluorimetry. Binding of immune complexes was ablated by inactivation of serum complement. In addition, the immunoglobulin in immune human serum blocked influenza binding to cells in the absence of complement, implying a minimal role for immunoglobulin‐Fc receptor interactions in this system. Significant immune complex binding required a threshold level of CD21 expression, suggesting that only those cells with the highest levels of CD21 are likely to participate in the processing of macromolecular antigens. B cells pulsed with complement‐influenza complexes elicited an augmented response from a panel of influenza‐specific, class II‐restricted T cell clones, as compared with those which had bound immunoglobulin‐influenza complexes lacking complement. This enhanced response did not require CD35. In addition, B cell lines expressing higher levels of CD21 were more efficient in processing antigen than those with lower levels. These findings suggest that presentation of antigen by B cells in immune individuals is dependent on the binding of complement‐antigen immune complexes to CD21.
Effect of exogenous application of sugars on the salt tolerance of perennial ryegrass protoplasts

Various sugars were introduced by electroporation into perennial ryegrass protoplasts, and the involvement of intracellular functional groups of the sugars in salt tolerance was investigated. The protoplasts were prepared from the young leaves of perennial ryegrass, and those into which sugars were introduced were treated with NaCl solution (250 mM, pH 7.0) for 6 h at 10°C. The survival rate of the protoplasts increased when xylitol, cellobiose, 1-kestose, maltose, maltotriose, raffinose and trehalose were introduced, while no changes occurred when fructose, fucose, galactose, glucose, inositol, mannitol, mannose, rhamnose, sorbitol, sorbose, fructobiose, lactose and sucrose were introduced. Cellobiose, 1-kestose, maltose, maltotriose, raffinose and trehalose possess a number of equatorial OH (e-OH) groups that promote the structuration of H2O. Xylitol, however, structures H2O even though it does not possess the e-OH groups. Hence, it is suggested that under conditions of NaCl stress, structured H2O protects the structure of cell membranes and the activity of enzymes, and that e-OH groups are involved in enhancing salt tolerance.
Cardiac actions of antihistamines.

Two of the nonsedating antihistaminic drugs, terfenadine and astemizole, have recently been recognized in rare cases to induce the syndrome of torsades de pointes, i.e. QT interval prolongation and life-threatening ventricular tachycardia. Each was found to prolong cardiac repolarization when its metabolic elimination was impaired, such as by liver disease or drugs that inhibit the 3A family of cytochrome P450. In vitro studies indicate that this action is due to blockade of one or more of the cardiac potassium channels that determine the duration of the action potential. Prescription guidelines are now available to reduce the risk of developing arrhythmias with these two drugs. Two agents recently marketed in the United States, Ioratidine and cetirizine, appear to lack the ability to prolong repolarization and induce torsades de pointes. Evaluation of the potential cardiac actions of investigational antihistamines is essential and may be of value for some of the older conventional agents.
Mutation of a Single CTCF Target Site within the H19 Imprinting Control Region Leads to Loss of Igf2 Imprinting and Complex Patterns of De Novo Methylation upon Maternal Inheritance

ABSTRACT The differentially methylated imprinting control region (ICR) region upstream of the H19 gene regulates allelic Igf2 expression by means of a methylation-sensitive chromatin insulator function. We have previously shown that maternal inheritance of mutated (three of the four) target sites for the 11-zinc finger protein CTCF leads to loss of Igf2 imprinting. Here we show that a mutation in only CTCF site 4 also leads to robust activation of the maternal Igf2 allele despite a noticeably weaker interaction in vitro of site 4 DNA with CTCF compared to other ICR sites, sites 1 and 3. Moreover, maternally inherited sites 1 to 3 become de novo methylated in complex patterns in subpopulations of liver and heart cells with a mutated site 4, suggesting that the methylation privilege status of the maternal H19 ICR allele requires an interdependence between all four CTCF sites. In support of this conclusion, we show that CTCF molecules bind to each other both in vivo and in vitro, and we demonstrate strong interaction between two CTCF-DNA complexes, preassembled in vitro with sites 3 and 4. We propose that the CTCF sites may cooperate to jointly maintain both methylation-free status and insulator properties of the maternal H19 ICR allele. Considering many other CTCF targets, we propose that site-specific interactions between various DNA-bound CTCF molecules may provide general focal points in the organization of looped chromatin domains involved in gene regulation.
The Prevalence and Pathogenicity of Propionibacterium acnes Keratitis

Purpose: To study the prevalence, pathogenicity, and virulence of Propionibacterium acnes keratitis. Methods: All cases of infectious keratitis submitted to the microbiologic laboratory of the New York Eye and Ear Infirmary between January 1, 2003, and April 6, 2006, were reviewed. Those cases in which P. acnes was recovered from culture were collected, and the medical records studied in depth. Results: Of 1555 cultures submitted to the microbiology laboratory, 1329 (85.5%) were positive for growth. One hundred twenty four (9.3%) of the 1329 cases yielded P. acnes in at least 1 culture medium. Seventy eight (62.9%) of 124 cases had not been pretreated with antibiotics before culture, and 66.7% of the nonpretreated ulcers were monomicrobial (P. acnes only). Fifty one (65.4%) of 78 cases of the nonpretreated corneal ulcers presented with a cellular reaction in anterior chamber, 12 (15.4%) with a hypopyon (6 were monomicrobial), 21 (26.9%) had stromal thinning (12 of which were monomicrobial), and 2 (2.6%) progressed to perforation (both polymicrobial). Corneal ulcers associated with P. acnes tended to be small (66.7%) and were widely distributed: central (n = 17, 21.8%), paracentral (n = 44, 56.4%), and peripheral (n = 17, 21.8%). The most common risk factors were contact lens wear and previous history of ocular surgery. Three of the 78 nonpretreated patients were unresponsive to medical treatment and required surgery for keratitis. Conclusion: This study provides evidence that P. acnes is a frequent cause of bacterial keratitis and may cause significant morbidity.
Mahogany (1377-1428) enters brain by a saturable transport system.

The mouse mahogany gene encodes a protein that is involved in the suppression of diet-induced obesity. We studied the ability of its widely conserved C-terminal fragment to cross the blood-brain barrier (BBB) in mice. Multiple-time regression analysis showed that the entry rate (K(i)) of (125)I-mahogany (1377-1428) from blood-to-brain was 5.5 x 10(-4) ml/g. min. After coinjection of unlabeled mahogany (1377-1428), the K(i) was significantly decreased, showing the self-inhibition characteristic of a saturable transport mechanism. The excess mahogany (1377-1428) did not change the influx rate of (99m)Tcalbumin, the vascular control, indicating a lack of disruption of the BBB. Statistically significant cross-inhibition was not seen with agouti-related protein (83-132), melanin-concentrating hormone, epidermal growth factor, leptin, a melanocortin-4 receptor antagonist, or alpha-melanocyte-stimulating hormone. HPLC showed that most of the injected (125)I-mahogany (1377-1428) reached the brain intact, and capillary depletion with washout showed that most of it reached the parenchyma. There was no brain-to-blood efflux system for mahogany (1377-1428) but rather retention after i.c. v. administration, and the octanol/buffer partition coefficient showed low lipophilicity. Thus, the results show that the C-terminal peptide product encoded by the mahogany gene crosses the BBB by a transport mechanism that is saturable. The ability of this system to be regulated indicates the therapeutic potential of mahogany (1377-1428) in the treatment of obesity.
Performance of nested PCR in the specific detection of Mycobacterium tuberculosis complex in blood samples of pediatric patients.

OBJECTIVE To evaluate the performance of nested PCR (nPCR) in detecting the Mycobacterium tuberculosis complex in blood samples of patients suspected of having TB, in order to determine its potential for use as an auxiliary tool in the laboratory diagnosis of TB in children. METHODS Detection of the M. tuberculosis complex in blood samples using as a target the insertion sequence IS6110 of the genomic DNA of the bacillus. Blood samples of 120 patients were evaluated. All of the patients were under 15 years of age at the time of their treatment at public hospitals in the city of Recife, Brazil (between January of 2003 and August of 2005). Attending physicians at the hospitals diagnosed TB based on the criteria recommended by the American Thoracic Society. The nPCR amplified a 123-bp fragment with outer oligonucleotides (IS1/IS2) and, in the subsequent reaction, using inner oligonucleotides (IS3/IS4), generating an 81-bp amplicon. RESULTS Active or latent TB was found in 65 patients, TB was ruled out in 28 suspected cases, and 27 patients were TB-free (controls). The sensitivity of nPCR was 26.15% and was significantly higher for the extrapulmonary form of the disease (55.56%) than for the pulmonary form (18.18%). The specificity was 92.73%. CONCLUSIONS Despite the difficulties in diagnosing TB in children and the low number of cases evaluated in the present study, nPCR in blood samples proved to be a rapid and specific technique, albeit one with low sensitivity. In order to establish its true usefulness in the diagnosis of paucibacillary forms, especially extrapulmonary TB, further studies need to be carried out with a larger sample of children and analyzing biological specimens other than blood.