Miracle-dz/UniFAR-FTUs huggingface dataset:
Time‐resolved backbone desolvation and mutational hot spots in folding proteins

A method is presented to identify hot mutational spots and predict the extent of surface burial at the transition state relative to the native fold in two‐state folding proteins. The method is based on ab initio simulations of folding histories in which transitions between coarsely defined conformations and pairwise interactions are dependent on the solvent environments created by the chain. The highly conserved mammalian ubiquitin is adopted as a study case to make predictions. The evolution in time of the chain topology suggests a nucleation process with a critical point signaled by a sudden quenching of structural fluctuations. The occurrence of this nucleus is shown to be concurrent with a sudden escalation in the number of three‐body correlations whereby hydrophobic units approach residue pairs engaged in amide‐carbonyl hydrogen bonding. These correlations determine a pattern designed to structure the surrounding solvent, protecting intramolecular hydrogen bonds from water attack. Such correlations are shown to be required to stabilize the nucleus, with kinetic consequences for the folding process. Those nuclear residues that adopt the dual role of protecting and being protected while engaged in hydrogen bonds are predicted to be the hottest mutational spots. Some such residues are shown not to retain the same protecting role in the native fold. This kinetic treatment of folding nucleation is independently validated vis‐a‐vis a Φ‐value analysis on chymotrypsin inhibitor 2, a protein for which extensive mutational data exists. Proteins 2002;47:447–457. © 2002 Wiley‐Liss, Inc.
D‐Dimer test in cancer patients with suspected acute pulmonary embolism

Summary. Background: The safety of a D‐dimer (DD) measurement in cancer patients with clinically suspected pulmonary embolism (PE) is unclear. Objectives: The aim of this study was to assess the accuracy of the DD test in consecutive patients with clinically suspected PE with and without cancer. Methods: The diagnostic accuracy of DD (Tinaquant D‐dimer) was first retrospectively assessed in an unselected group of patients referred for suspected PE (n = 350). Subsequently, the predictive value of the DD was validated in a group of consecutive inpatients and outpatients with clinically suspected PE prospectively enrolled in a management study (n = 519). The results of the DD test in cancer patients were assessed according to the final diagnosis of PE and the 3‐month clinical follow‐up. Results: In the first study group, DD showed a sensitivity and a negative predictive value (NPV) of 100% and 100% in patients with cancer and 97% and 98% in those without malignancy, respectively. In the validation cohort, the sensitivity and NPV of DD were both 100% (95% CI 82%–100% and 72%–100%, respectively), whereas in patients without malignancy, the corresponding estimates were 93% (95% CI 87%–98%) and 97% (95% CI, 95%–99%), respectively. The specificity of DD was low in patients with (21%) and without cancer (53%). Conclusions: A negative DD result safely excludes the diagnosis of PE in patients with cancer. Because of the low specificity, when testing 100 patients with suspected PE, a normal DD concentration safely excludes PE in 15 patients with cancer and in 43 patients without cancer.
Polymorphisms of the toll-like receptor 2 and 4 genes are associated with faster progression and a more severe course of sepsis in critically ill patients

Objective To determine whether the Arg753Gln polymorphism of the toll-like receptor 2 (TLR2) gene and the Asp299Gly polymorphism of the TLR4 gene in critically ill patients affect their clinical outcomes. Methods Medical and surgical patients in three intensive care units (ICU) were enrolled in this prospective study. TLR2 and TLR4 gene polymorphisms were determined using restriction fragment length polymorphism analysis. Results A total of 145 patients were included in this study: 28 patients carried heterozygous mutations (10 in the TLR2 gene, 19 in the TLR4 gene, and one combined) and 117 patients were wild type. Severe sepsis was observed in 33% of wild types (n = 38), 60% of the TLR2 group (n = 6), and 63% of the TLR4 group (n = 12); the difference was significant between the TLR4 and wild type groups. Both TLR groups demonstrated a shorter time-to-onset of severe sepsis or septic shock. Only the TLR4 group demonstrated significant progression towards septic shock compared with the wild type group. Length of ICU stay was significantly prolonged in the TLR4 group compared with the wild type group, but not in the TLR2 group. Conclusions Two common SNPs of the TLR2 and TLR4 genes – Arg753Gln and Asp299Gly – were associated with a shorter time-to-onset of severe sepsis or septic shock in patients admitted to the ICU.
Risk factor analysis and serological diagnosis of HIV‐1/HIV‐2 infection in a Brazilian blood donor population: validation of the World Health Organization strategy for HIV testing

Objective: To determine the relative prevalence of HIV‐1 and HIV‐2 and to evaluate the World Health Organization testing strategy for HIV diagnosis in a low‐risk population in Brazil. In addition, to assess risk factors for HIV infection. Design: Sera obtained from 9885 consecutive blood donors were screened in parallel by two HIV enzyme‐linked immunosorbent assays (ELISA) with different antigen composition and test principles (Ortho HIV‐1 and Wellcozyme HIV‐1/2). Samples reactive to either ELISA were submitted to a Western blot assay and to a rapid HIV‐1/2 ELISA (Sero‐Immuno Diagnostics). An ELISA test with specific HIV‐1/HIV‐2‐derived synthetic peptide was used to discriminate between samples reactive on the Wellcozyme HIV‐1/2 assay. Demographic and serological data were used to address risk factors for HIV infection. Results: All the 28 Western blot‐confirmed positive samples were reactive in both Ortho HIV‐1 and Wellcozyme HIV‐1/2 assays (sensitivity, 100%). The Wellcozyme HIV‐1/2 specificity (99.9%) was higher than Ortho HIV‐1 (99.5%). If sample reactivity to both tests was considered positive, the sensitivity and specificity of the screening would be 100%. However, further analysis with a third rapid HIV‐1/2 ELISA reduced both the sensitivity and the specificity of the sequential testing strategy. Discrimination between HIV‐1 and HIV‐2 showed evidence for the presence of HIV‐1 only. Finally, in the group aged 18–35 years, the presence of serological markers of hepatitis C virus and hepatitis B virus infections and the elevated levels of &bgr;2‐microglobulin were variables associated with the identification of HIV‐1‐seropositive blood donors. Conclusion: In a low‐risk population, application of two high quality ELISA tests with different antigens and test principles can replace the use of the Western blot. In addition to the cost being reduced by 10–16%, a rapid diagnosis and the absence of indeterminate Western blot results confer an advantage to this strategy.
Differences in Treatment Outcomes between Prescription Opioid-Dependent and Heroin-Dependent Adolescents

Objective:This study was designed to examine the extent to which heroin-dependent and prescription opioid-dependent adolescents experienced differential outcomes during a clinical trial designed to evaluate combined behavioral-pharmacological treatment. Methods:Participants were a volunteer sample of 36 adolescents who met DSM-IV criteria for opioid-dependence (ages 13–18 years eligible), 53% of which were heroin-dependent and 47% of which were dependent on prescription opioids used for nonmedical purposes. Participants received a 28-day, outpatient, medication-assisted withdrawal with the partial opioid agonist, buprenorphine, or the centrally active &mgr;-adrenergic blocker, clonidine, along with behavioral counseling and incentives contingent on opioid abstinence. Heroin-dependent and prescription opioid-dependent participants were compared on baseline characteristics and treatment outcomes, which included retention, opioid abstinence, HIV risk behavior, opioid withdrawal, and medication effects. Results:Heroin-dependent and prescription opioid-dependent youth had similar characteristics at intake. Heroin-dependent youth had higher baseline rates of drug-related HIV risk behavior and greater opioid withdrawal before receiving medication during treatment; however, this same group showed markedly greater improvements on these domains during treatment relative to prescription opioid-dependent youth. Both participant groups showed comparable outcomes based on clinically meaningful measures of treatment retention and opioid abstinence. Both heroin-dependent and prescription opioid-dependent youth who received buprenorphine experienced markedly better treatment outcomes relative to those who received clonidine. Conclusions:These results demonstrate that combined behavioral and buprenorphine treatment seems safe and efficacious in the treatment of both heroin-dependent and prescription opioid-dependent adolescents and provide novel information relating to treatment outcomes for these subgroups of opioid-dependent youth.
Treatment of pemphigus vulgaris with rituximab and intravenous immune globulin.

BACKGROUND Pemphigus vulgaris is a potentially fatal autoimmune mucocutaneous blistering disease. Conventional therapy consists of high-dose corticosteroids, immunosuppressive agents, and intravenous immune globulin. METHODS We studied patients with refractory pemphigus vulgaris involving 30% or more of their body-surface area, three or more mucosal sites, or both who had inadequate responses to conventional therapy and intravenous immune globulin. We treated the patients with two cycles of rituximab (375 mg per square meter of body-surface area) once weekly for 3 weeks and intravenous immune globulin (2 g per kilogram of body weight) in the fourth week. This induction therapy was followed by a monthly infusion of rituximab and intravenous immune globulin for 4 consecutive months. Titers of serum antibodies against keratinocytes and numbers of peripheral-blood B cells were monitored. RESULTS Of 11 patients, 9 had rapid resolution of lesions and a clinical remission lasting 22 to 37 months (mean, 31.1). All immunosuppressive therapy, including prednisone, could be discontinued before ending rituximab treatment in all patients. Two patients were treated with rituximab only during recurrences and had sustained remissions. Titers of IgG4 antikeratinocyte antibodies correlated with disease activity. Peripheral-blood B cells became undetectable shortly after initiating rituximab therapy but subsequently returned to normal values. Side effects that have been associated with rituximab were not observed, nor were infections. CONCLUSIONS The combination of rituximab and intravenous immune globulin is effective in patients with refractory pemphigus vulgaris.
Aberrant Interaction between Parkinson Disease-associated Mutant UCH-L1 and the Lysosomal Receptor for Chaperone-mediated Autophagy*

Parkinson disease (PD) is the most common neurodegenerative movement disorder. An increase in the amount of α-synuclein protein could constitute a cause of PD. α-Synuclein is degraded at least partly by chaperone-mediated autophagy (CMA). The I93M mutation in ubiquitin C-terminal hydrolase L1 (UCH-L1) is associated with familial PD. However, the relationship between α-synuclein and UCH-L1 in the pathogenesis of PD has remained largely unclear. In this study, we found that UCH-L1 physically interacts with LAMP-2A, the lysosomal receptor for CMA, and Hsc70 and Hsp90, which can function as components of the CMA pathway. These interactions were abnormally enhanced by the I93M mutation and were independent of the monoubiquitin binding of UCH-L1. In a cell-free system, UCH-L1 directly interacted with the cytosolic region of LAMP-2A. Expression of I93M UCH-L1 in cells induced the CMA inhibition-associated increase in the amount of α-synuclein. Our findings may provide novel insights into the molecular links betweenα-synuclein and UCH-L1 and suggest that aberrant interaction of mutant UCH-L1 with CMA machinery, at least partly, underlies the pathogenesis of PD associated with I93M UCH-L1.
Melatonin and Vitamin D Interfere with the Adipogenic Fate of Adipose-Derived Stem Cells

Adipose-derived stem cells (ADSCs) represent one of the cellular populations resident in adipose tissue. They can be recruited under certain stimuli and committed to become preadipocytes, and then mature adipocytes. Controlling stem cell differentiation towards the adipogenic phenotype could have a great impact on future drug development aimed at counteracting fat depots. Stem cell commitment can be influenced by different molecules, such as melatonin, which we have previously shown to be an osteogenic inducer. Here, we aimed at evaluating the effects elicited by melatonin, even in the presence of vitamin D, on ADSC adipogenesis assessed in a specific medium. The transcription of specific adipogenesis orchestrating genes, such as aP2, peroxisome proliferator-activated receptor γ (PPAR-γ), and that of adipocyte-specific genes, including lipoprotein lipase (LPL) and acyl-CoA thioesterase 2 (ACOT2), was significantly inhibited in cells that had been treated in the presence of melatonin and vitamin D, alone or in combination. Protein content and lipid accumulation confirmed a reduction in adipogenesis in ADSCs that had been grown in adipogenic conditions, but in the presence of melatonin and/or vitamin D. Our findings indicate the role of melatonin and vitamin D in deciding stem cell fate, and disclose novel therapeutic approaches against fat depots.
Mediastinal lymph node sampling following positron emission tomography with fluorodeoxyglucose imaging in lung cancer staging.

OBJECTIVES To evaluate the predictive accuracy as well as the rates of false-positive and false-negative results of CT and positron emission tomography (PET)-fluorodeoxyglucose (FDG) imaging in detecting the metastatic intrathoracic lymph nodes in patients with suspected or proven non-small cell lung cancer (NSCLC). Our other objective was to determine the need for routine invasive sampling procedure in confirming PET/CT staging results. METHODS The results of CT and PET-FDG scanning in 77 patients with suspected or proven NSCLC were correlated with the histologic findings of hilar/mediastinal lymph node sampling using mediastinoscopy, open biopsy, thoracotomy, or thoracotomy with resection. Patients were then classified into resectable and unresectable groups based initially on PET results and compared to histologic findings. RESULTS The sensitivity, specificity, and accuracy of CT and PET for detecting metastatic lymphadenopathy were 68%, 61%, 63%, and 87%, 91%, and 82%, respectively. A change of management with routine sampling following PET was seen in five of six patients (83%) with false-positive findings (13%) but in none of four patients (9%) with false-negative findings. CONCLUSION The false-positive findings of PET-FDG imaging affected selection of treatment in 83% of patients. However, false-negative results did not change management in any patient. This could potentially prevent unnecessary invasive thoracotomy, mediastinoscopy, or other sampling procedures in patients with negative PET results.
A Mouse Model for the Evaluation of Pathogenesis and Immunity to Influenza A (H5N1) Viruses Isolated from Humans

ABSTRACT During 1997 in Hong Kong, 18 human cases of respiratory illness, including 6 fatalities, were caused by highly pathogenic avian influenza A (H5N1) viruses. Since H5 viruses had previously been isolated only from avian species, the outbreak raised questions about the ability of these viruses to cause severe disease and death in humans. To better understand the pathogenesis and immunity to these viruses, we have used the BALB/c mouse model. Four H5N1 viruses replicated equally well in the lungs of mice without prior adaptation but differed in lethality for mice. H5N1 viruses that were highly lethal for mice were detected in multiple organs, including the brain. This is the first demonstration of an influenza A virus that replicates systemically in a mammalian species and is neurotropic without prior adaptation. The mouse model was also used to evaluate a strategy of vaccination against the highly pathogenic avian H5N1 viruses, using an inactivated vaccine prepared from nonpathogenic A/Duck/Singapore-Q/F119-3/97 (H5N3) virus that was antigenically related to the human H5N1 viruses. Mice administered vaccine intramuscularly, with or without alum, were completely protected from lethal challenge with H5N1 virus. Protection from infection was also observed in 70% of animals administered vaccine alone and 100% of mice administered vaccine with alum. The protective effect of vaccination correlated with the level of virus-specific serum antibody. These results suggests a strategy of vaccine preparedness for rapid intervention in future influenza pandemics that uses antigenically related nonpathogenic viruses as vaccine candidates.
Descending pathways to the spinal cord: A comparative study of 22 mammals

In order to estimate the qualitative commonalities and range of variation among major descending spinal pathways relevant to mankind's ancestral lineage, the supraspinal cell groups originating fibers descending directly to the spinal cord were examined in 22 mammalian species. In a standardized retrograde tract‐tracing procedure, flakes of raw HRP were applied directly to the freshly cut fibers of the spinal cord after it had been hemisected at the C1–C2 junction. After a 72‐hour survival period, brain and spinal cord tissues were processed by conventional HRP‐processing techniques.
Combined Hepatocellular–Cholangiocarcinoma: A Histopathologic, Immunohistochemical, and In Situ Hybridization Study

Combined hepatocellular–cholangiocarcinoma (CHC) forms a small but significant proportion of primary liver carcinomas. However, its diagnostic features are not well established, and this has possibly contributed to the variability in its reported clinical outcome in the literature. Many such tumors with features intermediate between hepatocellular carcinoma and cholangiocarcinoma (CC) may have been considered CC in the past based on positivity for “biliary differentiation” cytokeratins and the lack of availability of highly sensitive and specific hepatocellular markers. The utility of in situ hybridization for albumin mRNA, a recently available sensitive and specific hepatocellular marker, has not been reported in CHC. We investigated 27 CHCs with regard to their histomorphologic spectrum and association of these morphologies with immunohistochemical staining for different cytokeratins (CK7, CK19, and CK20; AE1; Cam 5.2), epithelial membrane antigen, polyclonal carcinoembryonic antigen and alpha-fetoprotein, and in situ hybridization for albumin mRNA. All 27 tumors contained areas morphologically intermediate between hepatocellular carcinoma and CC (transitional-type tumors), and in each case such areas formed at least 25% of the tumor. Nine (33%) tumors showed areas with “antler-like” morphology, a feature not previously described in CHC. Twenty-two of 23 tumors (96%) showed positive signals on in situ hybridization for albumin mRNA. Positivity for both hepatocellular (albumin mRNA) and biliary (keratin immunohistochemical profile) markers confirmed the light microscopic impression of biphenotypic differentiation in these tumors. Immunohistochemical positivity for all cytokeratins (except CK7) and epithelial membrane antigen, as well as the expression of albumin mRNA by in situ hybridization, did not show significant differences between hepatocellular carcinoma and CC-like areas. Based on the cytokeratin profile and results on polyclonal carcinoembryonic antigen/alpha-fetoprotein alone, many such tumors would be classified as CC. However, the positivity for albumin mRNA by in situ hybridization proves that such an interpretation would not have been accurate. Clinically, CHCs showed many differences from pure hepatocellular carcinoma, including the absence of cirrhosis (0 of 27), rarity of serum hepatitis B or C marker positivity (4 of 27), and normal to only mildly elevated serum alpha-fetoprotein levels (median 187 ng/mL). The tumor followed an aggressive clinical course, with overall 3-and 5-year survival rates of 30% and 18%, and in the resected cases of 38% and 24%, respectively.
Occupation-related allergies in dentistry.

BACKGROUND Allergies to natural rubber latex (NRL) were unknown in dentistry until 1987. That changed with the publication of a report documenting NRL-based anaphylaxis in a dental worker. This case and others prompted regulatory and manufacturing changes in rubber products and increased awareness throughout the profession. However, other common dental chemicals cause allergic reactions and irritation and often are handled with insufficient precautions. Although recognition of NRL allergy has improved, awareness of other potential allergens and irritants in dentistry still is limited. OVERVIEW Recent research indicates that the prevalence of NRL protein allergy may be decreasing. In contrast, occupation-related dermatoses associated with other dental products may be more common. Encounters with bonding agents, disinfectants, rubber, metals and detergents can cause occupation-based irritant contact dermatitis and allergic contact dermatitis. These conditions may be found in more than one-quarter of dental and medical personnel. Therefore, dental-specific information about the recognition and management of allergic and irritant reactions is needed. CONCLUSIONS AND CLINICAL IMPLICATIONS The prevalence of occupation-related dermatitis may be increasing in dentistry. Reducing exposure to potential irritants and allergens and educating personnel about proper skin care are essential to reversing this trend.
Structured treatment interruptions in HIV infection: benefit or disappointment?

Many investigators are and have been studying the impact of structured treatment interruptions in HIV patients on subsequent viral control, HIV-specific cellular and humoral immunity, improvement of quality of life, and reduction of side effects and costs. Although varying treatment schedules have been followed and few clinical trials of different cohort size have been completed, tentative conclusions can already be drawn. Firstly after the initiation of treatment during acute infection followed by structured treatment interruptions, some patients maintained low level viremia during many months, such control of viremia has not been observed after the initiation of treatment during chronic infection followed by structured treatment interruptions. Second, structured treatment interruptions lead to an increase in frequencies of HIV-specific CD8+ T-cell populations, however, these frequencies are not above pretreatment frequencies in chronically infected patients. Third, HIV-specific CD4+ T-cell responses can be induced or enhanced during structured treatment interruptions but this augmentation was usually only transient. Finally, selection of drug-resistant virus variants may occur during structured treatment interruptions but clinical resistance to treatment has been quite rare. The initial hopes that structured treatment interruptions would substantially enhance immune control in the absence of therapy have not been confirmed, particularly in patients who initiated therapy during chronic infection. Additional immune-stimulatory interventions are now being considered and tested, such as administration of cytokines or vaccination. Furthermore, the demonstration of reduced side effects or costs due to structured treatment interruptions awaits the completion of large, comparative studies with a follow-up of several years.