Miracle-dz/UniFAR-FTUs huggingface dataset:
Allelic loss at chromosomes 3p, 8p, 13q, and 17p associated with poor prognosis in head and neck cancer.

BACKGROUND Little is known about the molecular genetic events that contribute to the pathogenesis of squamous cell carcinoma of the upper aerodigestive tract. Previous molecular genetic studies have been limited to the identification of mutations of the p53 (also known as TP53) tumor suppressor gene, activation of a limited set of oncogenes, allelic loss at 3p and other locations, and occasional association with human papillomavirus infection. PURPOSE Our purpose was to screen tumor tissue and blood from patients with squamous cell carcinoma of the upper aerodigestive tract for loss of heterozygosity at polymorphic loci corresponding to each of the autosomal chromosomes and to identify the locations of additional putative tumor suppressor genes, other than RB (also known as RB1) and p53, that may contribute to the pathogenesis of this disease. METHODS Tumor tissue and blood were obtained from 68 consecutive patients with squamous cell carcinoma of the upper aerodigestive tract. In all cases, tumor tissue was obtained from the center of the surgical specimen. The relative absence of non-neoplastic tissue was confirmed by frozen-section histologic examination of immediately adjacent tissue. Initially, 30 paired tissue and blood samples were tested for loss of heterozygosity by polymerase chain reaction (PCR) to amplify 43 different highly polymorphic sequences containing small oligonucleotide repeats. After PCR amplification, with unique oligonucleotides flanking the repeat, visualization and sizing of the alleles on DNA sequencing gels were performed. Specific loss of heterozygosity was distinguished from random genetic loss due to generalized chromosomal instability if it occurred in more than 20% of specimens tested for a particular marker. RESULTS Significant loss of heterozygosity (> 20%) occurred at alleles at chromosome bands 3p21 (32%), 3p25-26 (56%), 8pter-21.1 (31%), 13q14 (27%), and 17p12 (45%). Loss of heterozygosity at more than two loci was significant with a poor prognosis (P = .039). CONCLUSIONS These findings demonstrate that squamous cell carcinoma of the upper aerodigestive tract exhibits genetic alterations at multiple loci and that allelic loss at more than two locations is indicative of a poor prognosis (the likelihood of the patient dying of disease). IMPLICATIONS While tumor suppressor genes at 3p (VHL), 13q (RB), and 17p (p53) have been identified, altered genes at other loci on 3p and on 8p have not yet been characterized. Furthermore, the genotype at these loci for squamous cell carcinoma of the upper aerodigestive tract has prognostic importance and may identify the patients who should receive the most aggressive treatment.
Humphrey matrix frequency doubling perimetry for detection of visual-field defects in open-angle glaucoma

Aim: Matrix perimetry uses frequency-doubling technology (FDT) incorporated into a 5° test target. This permits testing of the same number of locations within a defined visual field as standard automated perimetry (SAP) and may improve performance compared with original FDT perimetry. This study investigates the performance of Humphrey Matrix perimetry for detecting glaucomatous visual-field loss. Design: Prospective case control study. Methods: We recruited 115 participants with glaucomatous visual-field loss and 33 normal controls from an urban glaucoma practice. Each participant performed SITA 24-2 SAP then threshold 24-2 Matrix perimetry. Severity of visual-field loss was defined using SAP mean deviation (MD) as early (MD >−6 dB), moderate (MD −6 to −12 dB) or advanced (MD <−12 dB). The sensitivity and specificity of Humphrey Matrix perimetry were calculated for different automated indices. Results: The matrix perimetry sensitivity and specificity were up to 100% for moderate and advanced glaucomatous visual-field loss. A receiver operator characteristic area under the curve (AUC) analysis revealed MD to be slightly better than pattern standard deviation (PSD) for defining moderate (AUC: MD 0.997; PSD 0.987) and advanced defects (AUC: MD 1.000; PSD 0.987). Matrix was less sensitive (up to 87.3%) for detecting early glaucomatous visual-field loss compared with SITA 24-2 SAP (AUC: PSD 0.948; MD 0.910). Conclusions: Matrix perimetry is excellent for detection of moderate to advanced glaucomatous visual-field loss but may miss some early defects. It may be well suited to following progression of early to moderate field loss because of a smaller target size compared with original FDT perimetry.
Study in Tanzania of Impaired Glucose Tolerance: Methodological Myth?

During study of diabetes prevalence in six rural Tanzanian communities, a repeat oral glucose tolerance test (OGTT) was carried out in 514 subjects ≥ 15 yr of age within 1 wk of an initial 75-g OGTT. In 498 subjects, blood glucose was measured 2 h after the glucose load on both occasions, and in 175 subjects, fasting blood glucose measurement was also repeated. Of the 498 subjects, 245 had normal glucose tolerance in the first test and were selected at random for further testing; 223 subjects had impaired glucose tolerance (IGT), and 30 had diabetic values. Diabetes and IGT were diagnosed on the basis of the 2-h blood glucose values. In the second test, 241 (98.4%) of the 245 subjects with normal tolerance continued in this category and 4 (1.6%) showed IGT. Of the 223 with IGT in the first test, 171 (76.2%) reverted to normal on the second test, 7 (3.1%) had diabetic values, and 45 (20.2%) persisted with IGT. Of the 30 subjects diagnosed as diabetic in the first test, 8 (26.7%) remained with diabetic values, 11 (36.7%) had IGT, and 11 (36.7%) were normal. Based on the second test, the population-prevalence rates of diabetes and IGT would have been 0.5 and 3.3% vs. 1 and 7.6% based on the first test. There was a significant downward trend in the mean 2-h blood glucose values in all three diagnostic groups. Regression toward the mean could not account for the downward shift in blood glucose values observed on retesting. It is postulated that a phenomenon occurred similar to the acclimatizing reflex observed in measurement of blood pressure. Therefore, single 2-h postload values may be inadequate for the accurate assessment of IGT and diabetes-prevalence rates within communities, particularly those unused to blood sampling. Because of the instability of the category of IGT, it may be advisable to discontinue use of this term or to restrict the term to those who show impaired tolerance on more than one occasion.
Titanium alloy miniscrews for orthodontic anchorage: an in vivo study of metal ion release

PURPOSE: To examine and compare the levels of several metal ions released in the saliva of patients with orthodontic appliances, at different time points before and after insertion of a miniscrew. METHODS: Saliva of patients (n=20) was collected at four time points: before miniscrew placement (T1), 10 minutes (T2), 7 days (T3) and 30 days after miniscrew placement (T4). The salivary samples were analyzed by inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma optical emission spectrometry (ICP-OES). The release of nine different metal ions was observed: titanium (Ti), zinc (Zn), chromium (Cr), nickel (Ni), iron (Fe), copper (Cu), aluminum (Al), Vanadium (V) and cobalt (Co). Data were analyzed by descriptive statistics. Salivary metal concentrations from different time points of miniscrew treatment were compared using Wilcoxon paired tests (a=5%). RESULTS: At time point T4, there was a quantitative increase in the salivary concentration of Cu, Ti, V, Zn, as well as a quantitative decrease in the salivary concentration of Al, Co, Cr, Fe, Ni, when compared with T1. CONCLUSION: It can be concluded that the placement of fixed orthodontic appliances associated with miniscrews does not lead to an increase of salivary metal ion concentrations.
The rK39 immunochromatic dipstick testing: a study for K39 seroprevalence in dogs and human leishmaniasis patients for possible animal reservoir of cutaneous and visceral leishmaniasis in endemic focus of Satluj river valley of Himachal Pradesh (India).

BACKGROUND The newly recognized endemic focus of leishmaniasis in Satluj river valley of Himachal Pradesh (India) has both localized cutaneous leishmaniasis (LCL) and visceral leishmaniasis (VL) predominantly caused by Leishmania donovani. Rapid rK39 immunochromatographic dipstick test detects circulating antibodies to recombinant K39 antigen of L. donovani-infantum complex and is highly specific/sensitive in diagnosing symptomatic or asymptomatic infection in humans and dogs. METHODS The sera from two VL patients and 13 LCL patients, and 31 dogs were subjected to rK39 immunochromatographic dipstick testing with an aim to identify possible animal reservoir for leishmaniasis in this endemic focus. RESULTS AND CONCLUSION The positive rapid rK39 immunochromatographic dipstick test in 100% VL and 31.8% LCL patients, and 6.5% dogs suggests that both VL and LCL in this focus are apparently being caused by L. donovani-infantum and that reservoir infection is perhaps being chiefly maintained in asymptomatic dogs. However, it needs corroborative evidence in the form of in-vitro parasite cultivation and/or PCR studies for confirmation. A more elaborate study is recommended.
Validation of the Personal Need for Structure Scale in Chinese

To validate the Chinese version of the Personal Need for Structure Scale, questionnaires were administered to 1,418 individuals in three samples. Item-total correlations and internal consistency of the scale were acceptable. The test-retest reliability was . 79. Confirmatory factor analysis indicated that the Chinese version comprised two dimensions, as did the original version; Desire for Structure and Response to Lack of Structure. Correlation coefficients between the Personal Need for Structure Scale and other related measures indicated that the scale has acceptable discriminant validity and convergent validity.
Android: From Reversing to Decompilation

This talk deals with Android’s bytecode analysis. The Android system is now widespread, and lots of applications are developed each days. These applications are mostly written in Java, though it is possible to do calls to binaries or shared libraries. To be executed on the DVM the Java source code is translated into Java bytecode (.class files) and then a tool named ‘dx’ is used to convert it into the Dalvik format (.dex files). Such a conversion is needed as the DVM is a register-based machine whereas the JVM is a stack-based one, and as such they have different opcodes. Due to the nature of the bytecode, its reversing is somewhat easier than machine code. Indeed, unlike machine code, (Dalvik) bytecode contains semantic information that allows us to do a better analysis. We can get useful details on variables, fields, methods. We can create signatures for a method, or we can use the android permissions to see where a specific one is used in an application. The analysis part allows us to extract the control flow graph (which is composed of basic blocks, and which cannot be modified dynamically due to the virtual machine) which is used to represent the different possibles paths of an application. Furthermore, we have implemented new algorithms to calculate the similarity distance between two applications, a useful information to know if your application has been stolen from the android market. It’s also possible to use similarity to do ‘diffing’ of Android applications is useful to see patches of bugs or insertion of evil code, this is why we have developed a combination of techniques to quickly see the differences between two applications. Moreover it’s interesting to have the ability to manipulate in a simple way all these new formats (APK, DEX, Dalvik bytecode, Android’s binary xml) to automate testing directly in a program or in a specific interpreter. There are some ways to retrieve the Java source code of an application from the bytecode, for instance some people use a software which transforms Dex bytecode into Java bytecode and then combine it with a regular Java decompiler. But the resulting code often looks like an obfuscated version which does not compile than real source code. That’s why we developed a new decompiler which uses only Dalvik bytecode to create an original Java source code. We present a new open-source tool (Androguard) written in Python (and some parts of C language) which help the reversing of Android applications, as well as our decompiler.
Accuracy of Schneiderian membrane thickness: a cone‐beam computed tomography analysis with histological validation

OBJECTIVES Cone-beam computed tomography (CBCT) has been used in the literature to evaluate Schneiderian membrane thickness (SMT), but its accuracy has never been validated. The primary aim of this study was to compare the SMT measured by CBCT to the gold standard histological assessment. The correlations between SMT and anatomical structures of the maxillary sinus and alveolar bone were also tested. MATERIALS AND METHODS Fourteen fresh cadaver heads were used for the study, and 28 sinus lift augmentation procedures were performed to obtain the membrane samples. Samples were fixed in formalin and stained with hematoxylin-eosine and Masson trichrome. Specimens were measured by optic microscope at three points, and a mean was obtained. Anatomical landmarks were used to accurately position the CBCT slice, so the SMT could be measured in predetermined locations. Wilcoxon signed-rank test was used to compare values of histological and CBCT measurements, and Spearman's correlation coefficient was calculated to examine the relationship between thickness and anatomical parameters. RESULTS A total of 597 histological measurements were performed, and the mean SMT thickness was 0.30 ± 0.17 mm. The mean CBCT membrane thickness was 0.79 ± 0.52 mm. A statistically significant difference from histological and radiological readings was observed (P = 0.000). Interestingly, 87.77% histological measurements had membrane less than 0.5 mm in thickness compared to 26.66% in CBCT assessment. CONCLUSIONS Within the limitation of this study, the median histological Schneiderian membrane thickness was 0.30 mm. Cone-beam computed tomography assessment was 2.6 times higher than the histological examination.
Glomeruloid Hemangioma A Distinctive Cutaneous Lesion of Multicentric Castleman's Disease Associated with POEMS Syndrome

A histologically distinctive cutaneous hemangioma occurring in two patients with biopsy-proven multicentric Castleman's disease associated with POEMS (polyneuropathy, organomegaly, endocrinopathy, M-protein, skin changes) syndrome are reported. The lesions were multiple, and appeared as red to purple papules over the trunk and proximal limbs. Microscopically, ectatic dermal vascular spaces were seen filled with aggregates of capillaries, resulting in structures reminiscent of renal glomeruli. Interspersed between the blood-filled capillary loops were plump “stromal” cells possessing clear vacuoles and periodic acid-schiff-positive eosinophilic globules. These cells had the immunohistochemical profile of endothelial cells (positivity for factor VIII-related antigen, and negativity for leukocyte common antigen, macrophage marker, and muscle-specific actin), and probably represented immature elements that had accumulated immunoglobulins and other proteinaceous material from the circulation. Because vascular lesions may appear before the full-blown POEMS syndrome develops, we suggest careful evaluation and follow-up of all patients presenting with glomeruloid hemangioma or cherry-type capillary hemangioma with focal glomeruloid features for potential development of this syndrome.
Coordination of cytochrome c oxidase gene expression in the remodelling of skeletal muscle

SUMMARY Many fish species respond to low temperature by inducing mitochondrial biogenesis, reflected in an increase in activity of the mitochondrial enzyme cytochrome c oxidase (COX). COX is composed of 13 subunits, three encoded by mitochondrial (mt)DNA and 10 encoded by nuclear genes. We used real-time PCR to measure mRNA levels for the 10 nuclear-encoded genes that are highly expressed in muscle. We measured mRNA levels in white muscle of three minnow species, each at two temperatures: zebrafish (Danio rerio) acclimated to 11 and 30°C, goldfish (Carassius auratus) acclimated to 4 and 35°C, and northern redbelly dace (Chrosomus eos) collected in winter and summer. We hypothesized that temperature-induced changes in COX activity would be paralleled by COX nuclear-encoded subunit transcript abundance. However, we found mRNA for COX subunits showed pronounced differences in thermal responses. Though zebrafish COX activity did not change in the cold, the transcript levels of four subunits decreased significantly (COX5A1, 60% decrease; COX6A2, 70% decrease; COX6C, 50% decrease; COX7B, 55% decrease). Treatments induced changes in COX activity in both dace (2.9 times in winter fish) and goldfish (2.5 times in cold fish), but the response in transcript levels was highly variable. Some subunits failed to increase in one (goldfish COX7A2, dace COX6A2) or both (COX7B, COX6B2) species. Other transcripts increased 1.7–100 times. The most cold-responsive subunits were COX4-1 (7 and 21.3 times higher in dace and goldfish, respectively), COX5A1 (13.9 and 5 times higher), COX6B1 (6 and 10 times higher), COX6C (11 and 4 times higher) and COX7C (13.3 and 100 times higher). The subunits that most closely paralleled COX increases in the cold were COX5B2 (dace 2.5 times, goldfish 1.7 times) and COX6A2 (dace 4.1 times, goldfish 1.7 times). Collectively, these studies suggest that COX gene expression is not tightly coordinated during cold-induced mitochondrial remodelling in fish muscle. Further, they caution against arguments about the importance of transcriptional regulation based on measurement of mRNA levels of select subunits of multimeric proteins.
Multitrophic interactions and the diamondback moth : implications for pest management

There is a scarcity of studies concerning Plutella xylostella L. dealing with either interactions between partial plant resistance and insecticides or multitrophic interactions (with or without insecticides). Such studies are vital to allow improved understanding of possible interactions in IPM programmes and may help both to develop approaches which enhance cultural and biological controls and minimise insecticide use. Laboratory studies showing the relationship between different degrees of partial plant resistance to P. xylostella (in various Brassica oleracea var. capitata L. and B. pekinensis (Lour.) Rupr. cultivars), leaf biomass consumption, leaf surface area damage and residual toxicity of two selective insecticides are presented and reasons for consistent relationships between various factors are discussed. Insecticide toxicity to P. xylostella larvae on plants with partial plant resistance is shown to be less compared with insecticides applied to either more or less resistant plants. Tritrophic laboratory and field studies in Malaysia show that larvae of P. xylostella on different host plant species and cultivars may experience different and sometimes contrasting rates of relative survival and parasitism by the key endolarval hymenopteran parasitoids, Diadegma semiclausum Hellén and Cotesia plutellae Kurdj. Finally, the value of multitrophic studies is discussed and their potential for stimulating novel strategies is considered.
Positive selection and high sensitivity test for MYD88 mutations using locked nucleic acid

Detection of mutations in the myeloid differentiation primary response gene 88 (MYD88) has clinical implications on diagnosis and therapy, especially in patients with Waldenström's macroglobulinemia (WM) and IgM monoclonal gammopathy of unknown significance (IgM‐MGUS). We describe a method that provides greatly increased sensitivity for detecting minority mutations in MYD88.
Suberosis: clinical study and new etiologic agents in a series of eight patients.

BACKGROUND Penicillium frequentans is considered to be the causal agent of suberosis, hypersensitivity pneumonitis due to cork dust inhalation. Nevertheless, other fungi can colonize cork during its storage period in humid conditions. The aims of the study were to assess the etiologic role of several fungi and cork itself in the genesis of suberosis, and to review the clinical characteristics of patients with this disease. METHODS Eight patients with suberosis were studied. Chest radiography, high-resolution chest CT, pulmonary function testing, bronchofibroscopy with BAL and transbronchial biopsy, and delayed cutaneous hypersensitivity tests were performed. Fungal and suberin (cork that is culture negative for fungi) antigens were used for serum determination of specific IgG antibodies, immediate hypersensitivity specific skin tests, and specific bronchial challenge tests. RESULTS Serum specific IgG antibody determinations and specific skin tests against Aspergillus fumigatus and suberin demonstrated the capacity of both these antigenic extracts to induce an immunologic response. Positive specific bronchial challenge tests performed not only with P frequentans but also with A fumigatus, and cork itself were recorded in some patients for the first time in this disease. Dyspnea and cough were the most frequent symptoms. Clinical and functional improvement occurred after antigen avoidance. CONCLUSIONS In addition to P frequentans, A fumigatus and cork dust itself may contribute to the development of suberosis.
A 12b 500MS/s DAC with >70dB SFDR up to 120MHz in 0.18μm CMOS

A CMOS current steering 12b 500MS/s 216mW DAC without any additional circuitry to remove errors introduced during the conversion process has >70dB SFDR up to 120MHz above the Nyquist band. This is comparable to state-of-the-art performance requiring additional circuitry, and better than any design without additional circuitry
Trafficking determinants for PfEMP3 export and assembly under the Plasmodium falciparum‐infected red blood cell membrane

During the maturation of intracellular asexual stages of Plasmodium falciparum parasite‐encoded proteins are exported into the erythrocyte cytosol. A number of these parasite proteins attach to the host cell cytoskeleton and facilitate transformation of a disk‐shaped erythrocyte into a rounded and more rigid infected erythrocyte able to cytoadhere to the vasculature. Knob formation on the surface of infected erythrocytes is critical for this cytoadherence to the host endothelium. P. falciparum proteins have been identified that localize to the parasite‐infected erythrocyte membrane: the variant cytoadherence ligand erythrocyte membrane protein 1 (PfEMP1), the knob‐associated histidine‐rich protein (KAHRP) and the erythrocyte membrane protein 3 (PfEMP3). In this study, we have generated parasites expressing PfEMP3‐green fluorescent protein chimeras and identified domains involved in entry to the secretory pathway, export across the parasitophorous vacuolar membrane and attachment to Maurer's clefts and the erythrocyte membrane. Solubility assays, fluorescence photobleaching experiments and immunogold electron microscopy suggest that the exported chimeric proteins are trafficked in a complex rather than in vesicles. This study characterizes elements involved in the tight but transient binding of PfEMP3 to Maurer's clefts and shows that the same elements are necessary for correct assembly under the erythrocyte membrane.