Efficient Approximate Kernel Based Spike Sequence Classification

Machine learning (ML) models, such as SVM, for tasks like classification and clustering of sequences, require a definition of distance/similarity between pairs of sequences. Several methods have been proposed to compute the similarity between sequences, such as the exact approach that counts the number of matches between k-mers (sub-sequences of length k) and an approximate approach that estimates pairwise similarity scores. Although exact methods yield better classification performance, they pose high computational costs, limiting their applicability to a small number of sequences. The approximate algorithms are proven to be more scalable and perform comparably to (sometimes better than) the exact methods - they are designed in a "general" way to deal with different types of sequences (e.g., music, protein, etc.). Although general applicability is a desired property of an algorithm, it is not the case in all scenarios. For example, in the current COVID-19 (coronavirus) pandemic, there is a need for an approach that can deal specifically with the coronavirus. To this end, we propose a series of ways to improve the performance of the approximate kernel (using minimizers and information gain) in order to enhance its predictive performance pm coronavirus sequences. More specifically, we improve the quality of the approximate kernel using domain knowledge (computed using information gain) and efficient preprocessing (using minimizers computation) to classify coronavirus spike protein sequences corresponding to different variants (e.g., Alpha, Beta, Gamma). We report results using different classification and clustering algorithms and evaluate their performance using multiple evaluation metrics. Using two datasets, we show that our proposed method helps improve the kernel's performance compared to the baseline and state-of-the-art approaches in the healthcare domain.

Efficacy of pentamidine-loaded chitosan nanoparticles as a novel drug delivery system for Leishmania tropica

The present study compares the in vitro effects of nanoparticles loaded pentamidine drug and conventional pentamidine on Leishmania tropica. Herein, pentamidine-loaded chitosan nanoparticles (PTN-CNPs) have been synthesized through an ionic gelation method with sodium tripolyphosphate (TPP). Next, the physical characteristics of PTN-CNPs were determined through the surface texture, zeta potential, in vitro drug release, drug loading content (DLC), and encapsulation efficacy (EE) and compared its efficacy with free pentamidine (PTN) drug against promastigotes and axenic amastigotes forms of L. tropica in vitro. The PTN-CNPs displayed a spherical shape having a size of 88 nm, an almost negative surface charge (-3.09 mV), EE for PTN entrapment of 86%, and in vitro drug release of 92% after 36 h. In vitro antileishmanial activity of PTN-CNPs and free PTN was performed against Leishmania tropica KWH23 promastigote and axenic amastigote using 3-(4, 5- dimethylthiazol-2-yl)-2, 5-diphenyletetrazolium bromide (MTT) assay. It was observed that the effect of PTN-CNPs and free PTN on both forms of the parasite was dose and time dependent. Free PTN presented low efficacy even at higher dose (40 µg/ml) with 25.6 ± 1.3 and 26.5 ±1.4 mean viability rate of the promastigotes and axenic amastigotes, respectively after 72 hrs incubation. While PTN-CNPs showed strong antileishmanial effects on both forms of parasite with 16 ± 0.4 and 19 ± 0.7 mean viability rate at the same higher concentration (40 µg/ml) after 72 hrs incubation. Half maximal inhibitory concentration (IC50) values of PTN-CNPs toward promastigotes and amastigotes were obtained as 0.1375 µg/ml and 0.1910 µg/ml, respectively. In conclusion, PTN-CNPs effectively inhibited both forms of the L. tropica; however, its effect was more salient on promastigotes. This data indicates that the PTN-CNPs act as a target drug delivery system. However, further research is needed to support its efficacy in animal and human CL.

Frozen-thawed gelatin-induced osteogenic cell sheets of canine adipose-derived mesenchymal stromal cells improved fracture healing in canine model

We assessed the efficacy of frozen-thawed gelatin-induced osteogenic cell sheet (FT-GCS) compared to that of fresh gelatin-induced osteogenic cell sheet (F-GCS) with adipose-derived mesenchymal stromal cells (Ad-MSCs) used as the control. The bone differentiation capacity of GCS has already been studied. On that basis, the experiment was conducted to determine ease of use of GCS in the clinic. In vitro evaluation of F-GCS showed 3–4 layers with an abundant extracellular matrix (ECM) formation; however, cryopreservation resulted in a reduction of FT-GCS layers to 2–3 layers. Cellular viabilities of F-GCS and FT-GCS did not vary significantly. Moreover, there was no significant difference in mRNA expressions of Runx2, β-catenin, OPN, and BMP-7 between F-GCS and FT-GCS. In an in vivo experiment, both legs of six dogs with transverse radial fractures were randomly assigned to one of three groups: F-GCS, FT-GCS, or control. Fracture sites were wrapped with the respective cell sheets and fixed with 2.7 mm locking plates and six screws. At 8 weeks after the operations, bone samples were collected and subjected to micro computed tomography and histopathological examination. External volumes of callus as a portion of the total bone volume in control, F-GCS, and FT-GCS groups were 49.6%, 45.3%, and 41.9%, respectively. The histopathological assessment showed that both F-GCS and FT-GCS groups exhibited significantly (p < 0.05) well-organized, mature bone with peripheral cartilage at the fracture site compared to that of the control group. Based on our results, we infer that the cryopreservation process did not significantly affect the osteogenic ability of gelatin-induced cell sheets.

Evaluating fertility and growth rate potential of indigenous sheep breeds submitted to heat stress under different management systems

Objective:

Sheep farming is an important source of livelihood in the southern Khyber Pakhtun Khwa province of Pakistan where they are reared under extensive system (ES). This system has limitations of improper feeding, rearing, and management which negatively affect their productivity. The present study compares different rearing systems and their stresses on fertility, behavior, and growth rate potential of two sheep breeds of Pakistan.

Materials and Methods:

Eighty ewes were selected; forty each from Damani and Balkhi breeds reared in semi-intensive system (SIS) and ES at Paharpur district, Dera Ismail Khan. Blood samples were collected in triplicate on days 0, 14, and 28 of May, and the molecular and behavioral stress, growth, and fertility rates were recorded.

Results:

The highest growth and fertility rate were observed in both the breeds in SIS than in ES (p < 0.01). The values of stress indicators (cortisol, heat shock protein (HSP-70)) and behavioral stress parameters were found lower in Damani breed as compared to Balkhi breed in both rearing systems (p < 0.01). All the molecular stress and behavioral stress parameters were negatively associated with metabolic hormones (T3 and T4) (p < 0.01). A positive correlation was observed among all the molecular stress and behavioral stress parameters (p < 0.01). Similarly, T3 and T4 were positively interlinked to one another (p < 0.01).

Conclusion:

It was concluded that both Damani and Balkhi sheep showed lower stress levels and better fertility and growth parameter in SIS than ES system of rearing. Local Damani breed exhibited well tolerant ability and genetic adaptation to the local environment as compared to Balkhi breed.

Application of tuned liquid column ball damper (TLCBD) for improved vibration control performance of multi-storey structure

Tuned liquid column ball damper (TLCBD) is a passive control device used for controlling the building vibrations induced from wind or earthquakes. TLCBD is a modified form of conventional tuned liquid column damper (TLCD). This paper studies the effect of TLCBD on the four-storey steel frame structure. The performance of the TLCBD is also compared with conventional TLCD. The analytical model of both TLCD and TLCBD is presented here. The effectiveness of these analytical models is examined experimentally by series of shaking table tests under different excitation levels including harmonic loadings and seismic excitations. In TLCBD, the vibration is reduced significantly as compared to TLCD by using steel ball as a moving orifice. The difference in diameter of steel ball and tube, containing the liquid column, acts as an orifice which moves with the movement of the ball. This moving orifice phenomenon enhanced the vibration reduction effect by resisting the water motion in the TLCBD. Root mean square (RMS) and peak values of acceleration were calculated for each loading and each storey of uncontrolled and controlled structures. Comparison of the time histories of controlled and uncontrolled structures for different loadings is also reported. Results indicate that the TLCBD is more effective in the earthquake scenarios as compared to the harmonic excitations. The TLCBD controls the vibration of the primary structure significantly in vibration reduction.

Selenium-enriched probiotics improve hepatic protection by regulating pro-inflammatory cytokines and antioxidant capacity in broilers under heat stress conditions

Objective:

High ambient temperature in poultry is a challenging and fatal stress among environmental factors. It affects the production quality, damages the liver, and increases mortality in broilers. The present study is focused to explore appropriate utilization of Selenium (Se) as a feed additive in broiler chickens against high temperature.

Materials and Methods:

Day-old male broiler chickens (Ross 308) (n = 200) were grouped according to the supplements used in their basal diets such as: corn-soybean basal diet as control (Con), a basal diet containing sodium selenite, basal diet with probiotics, and a basal diet containing selenium-enriched probiotics (SP). At the end of the experimental period of 42 days, the liver was isolated and was used to determine the antioxidant capacity through a spectrophotometer. Inflammatory and anti-inflammatory cytokines production in the liver was measured through a real-time polymerase chain reaction.

Results:

Hepatic analyses revealed the decreased level of malondialdehyde, whereas glutathione, glutathione peroxidase (GSH-Px), and superoxide dismutase levels were increased in the SP group. Furthermore, supplementation of SP significantly up-regulated the mRNA expression of glutathione peroxidase 1 (GPx1), GPx4, IL6, and IL10 and down-regulated the expression of pro-inflammatory cytokines.

Conclusion:

It is thus concluded that SP as a potential nutritive supplement may facilitate hepatic protection by suppressing hepatic oxidation, inflammation, and necrosis during the high ambient temperature of summer.

Improved Healing after the Co-Transplantation of HO-1 and BDNF Overexpressed Mesenchymal Stem Cells in the Subacute Spinal Cord Injury of Dogs

Abundant expression of proinflammatory cytokines after a spinal cord injury (SCI) creates an inhibitory microenvironment for neuroregeneration. The mesenchymal stem cells help to mitigate the inflammation and improve neural growth and survival. For this purpose, we potentiated the function of adipose-derived mesenchymal stem cells (Ad-MSCs) by transfecting them with brain-derived neurotrophic factor (BDNF) and heme oxygenase-1 (HO-1), through a lentivirus, to produce BDNF overexpressed Ad-MSCs (BDNF-MSCs), and HO-1 overexpressed Ad-MSCs (HO-1-MSCs). Sixteen SCI beagle dogs were randomly assigned into four treatment groups. We injected both HO-1 and BDNF-overexpressed MSCs as a combination group, to selectively control inflammation and induce neuroregeneration in SCI dogs, and compared this with BDNF-MSCs, HO-1-MSCs, and GFP-MSCs injected dogs. The groups were compared in terms of improvement in canine Basso, Beattie, and Bresnahan (cBBB) score during 8 weeks of experimentation. After 8 weeks, spinal cords were harvested and subjected to western blot analysis, immunofluorescent staining, and hematoxylin and eosin (H&E) staining. The combination group showed a significant improvement in hindlimb functions, with a higher BBB score, and a robust increase in neuroregeneration, depicted by a higher expression of Tuj-1, NF-M, and GAP-43 due to a decreased expression of the inflammatory markers interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), and an increased expression of interleukin-10 (IL-10) (P ≤ 0.05). H&E staining showed more reduced intraparenchymal fibrosis in the combination group than in other groups (P ≤ 0.05). It was thus suggested that the cotransplantation of HO-1 and BDNF-MSCs is more effective in promoting the healing of SCI. HO-1-MSCs reduce inflammation, which favors BDNF-induced neuroregeneration in SCI of dogs.

Gelatin positively regulates the immunosuppressive capabilities of adipose-derived mesenchymal stem cells

This characteristics of adipose-derived mesenchymal stem cells (Ad-MSCs) can be selectively enhanced by altering the culture environment. We evaluated the effects of gelatin on Ad-MSCs when used in combination with culture media. Ad-MSCs were initially cultured in 0%, 0.5%, 1%, 2%, and 4% gelatin in Dulbecco's modified Eagle's medium (DMEM) to evaluate cell proliferation. This expression of inflammatory, antiinflammatory, antioxidant, and osteogenic markers was then assessed by rtPCR in Ad-MSCs cultured in 0.5% gelatin in DMEM (GMSCs), and without gelatin (MSCs), for 5 and 10 days. We found that 0.5% gelatin significantly increased the proliferation rate of Ad-MSCs after 24 h of incubation, up until 72 h. GMSCs had upregulated IL-10, VEGF, and HO-1 after 5 and 10 days of incubation, while IL-6 and TNF-α were upregulated after 5 days and then significantly decreased after 10 days of incubation. The osteogenic factors BMP-7, AXIN, and β-catenin were significantly upregulated in GMSCs after 5 and 10 days. Notably, there was 5- to 8-fold higher expression of BMP-7 in GMSCs than in MSCs. We conclude that culture medium containing 0.5% gelatin enhances the proliferation rate, induces immunosuppression, and activates BMP-7 and the wnt/AXIN/β-catenin pathway in Ad-MSCs.

The use of Acufex Wedge Tag Tissue Anchors in Hand Surgery

Over a period of 4 years, in various circumstances commonly seen in hand surgery, 100 patients underwent 127 soft tissue attachments to bone using the Acufex wedge tag system (Acufex Microsurgical, Inc, Mansfield, MA), a non-metallic bone anchor. No failures to maintain the attachment of the desired soft tissue to bone were identified. While less robust than the Mitek anchor, the other commonly available system of bone anchoring, and therefore possibly inappropriate for general orthopaedics, the Acufex wedge tag proved adequate for the smaller forces of hand surgery.

Retrospective analysis of abdominal surgeries at Nepalgunj Medical College (NGMC), Nepalgunj, Nepal: 2 year's experience

BACKGROUND

Abdominal surgeries are the commonest major operations that are performed in the department of surgery.

AIM

To find out the different causes of emergency and elective abdominal surgeries at Nepalgunj Medical College Teaching Hospital (NGMCTH) Nepalgunj, Nepal.

MATERIAL AND METHOD

This is a retrospective study conducted in the department of surgery at NGMCTH Nepalgunj, Nepal, over a period of 2 years (2001 to 2003). The patients included in this study were drawn from Banke, Bardiya, Kailali, Kanchanpur, Surkhet, Dang, Dailake, and Tikapur. They belong to both sexes and different age groups. All the records of these patients under went laparotomy for elective as well as emergency conditions were included in this study. The data were analyzed; tabulated and following results were obtained.

RESULTS

The commonest cause of emergency laparotomies were peritonitis (peptic ulcer, enteric and appendicular perforations) whereas, the commonest cause of elective laparotomies were chronic cholecystitis with cholelithiasis followed by chronic appendicitis and pyloric obstruction.

CONCLUSION

Over all, cholecystectomy for cholecystitis with cholelithiasis was the commonest operation, which was done in last two years. This disease may be because of excessive use of saturated animal fat and vegetable oil. Peritonitis was the 2nd commonest cause of abdominal surgery. Among the causes of peritonitis, peptic ulcer perforations were the frequent followed by enteric and appendicular perforations. Appendicitis was the 3rd commonest cause of abdominal surgery. Nepal, being a Hindu country, people consume excessive amount of meat, and possibly due to this, the disease of the appendix was very high as compared to other Asian countries where people live on bulk cellulose diet.

VON RECKLINGHAUSEN'S DISEASE

Von Recklinghausen's disease (VRD) is a rare genetic autosomal dominant disorder that affects the ectodermaltissues (nerve and skin). The cardinal features of this disorder are spots of increase pigmentation (cafe-au-lait spot, CAL), peripheral nerve tumours (neurofibromatosis) and iris hamartoma (Lisch nodule). Clinicaldiagnosis of VRD is based on the criteria given by National Institute of Health (NIH) because the mutationanalysis is laborious. Here, we are reporting a case of a family with VRD.Key Words: VonRecklinghausen's disease (VRD), Cafe-au-lait (CAL) spot, Lisch nodule,Neurofibromatosis (NF)

Identification and epidemiological characterization of Streptococcus uberis isolated from bovine mastitis using conventional and molecular methods

In the present study 130 S. uberis strains and one S. parauberis strain isolated from bovine milk samples of 58 different farms of various locations in Hesse, Germany, as well as two reference strains of each species were comparatively investigated for cultural, biochemical, serological and molecular properties. All S. uberis strains produced the enzyme beta-D-glucuronidase, while the S. parauberis strains were negative. The S. uberis and S. parauberis 16S rRNA genes were amplified by polymerase chain reaction and subsequently digested with the restriction enzymes RsaI and AvaII yielding species-specific restriction patterns. Both species were additionally identified by amplifying species-specific parts of the genes encoding the 16S rRNA, the 23S rRNA and the 16S-23S rDNA intergenic spacer region, respectively. The CAMP factor gene cfu, a potential virulence factor of S. uberis, was amplified, corresponding to a phenotypically positive CAMP-reaction, using cfu-specific oligonucleotide primers. In addition the streptokinase/plasminogen activator encoding genes skc/pauA, a second potential virulence factor, could be amplified for 126 of the 130 S. uberis but not for S. parauberis. A DNA fingerprinting of S. uberis strains, performed by macrorestriction analysis of their chromosomal DNA by pulsed-field gel electrophoresis, revealed that most of the isolates were not related to each other. However, identical DNA patterns were noted for some of the isolates within different quarters of an individual cow and also for different cows within the same farm. The generally unrelated DNA patterns indicated that S. uberis is a pathogen with multiple environmental habitats and that infections are caused by a great variety of strains.

Identification of Streptococcus dysgalactiae strains of Lancefield's group C, G and L by polymerase chain reaction

Streptococcus dysgalactiae serogroup C, G and L strains were investigated by polymerase chain reaction (PCR) using oligonucleotide primers designed according to species-specific parts of the 16S-23S rDNA intergenic spacer region. The oligonucleotide primers with specificity for the 16S-23S rDNA intergenic spacer region allowed a correct identification of all S. dysgalactiae serogroups C, G and L strains investigated. No cross-reactivities could be observed with any of the control strains indicating the usefulness of PCR-technology to identify the serologically heterogeneous species S. dysgalactiae.

Prospective study of pattern of breast diseases at Nepalgunj Medical College (NGMC), Nepal

INTRODUCTION

Patients of breast diseases of female are very common cases attending surgical out patient department for treatment at NGMC, Banke, Nepal.

OBJECTIVES

To find out the magnitude of the breast diseases, its frequency distribution in different age group among the patients attending surgical OPD for surgical consultation.

MATERIAL AND METHOD

This is a prospective study conducted at NGMC, Nepalgunj, Nepal. Patients attending surgical OPD for one or another breast problem were included. They were assessed clinically and their diagnosis was confirmed by cytological (FNAC) or histopathological (biopsy) examination. Then they were subjected to appropriate treatment. It must be mentioned at the outset that no clinical mammography could be done in the case of this study as these facilities are not available at NGMC.

RESULTS

264 cases of breast disease were diagnosed. This includes 232 female and 32 male patients. The ratio between benign and malignant lesions was 13.6:1. The benign breast diseases (BBD) were the commonest lesions of the breast found in this study (93.2%) whereas malignant lesion was infrequent (6.8%). Among BBD, the commonest lesion was fibroadenoma (32.57%) followed by breast abscess (24.19%), Aberration of Normal Development and Involution (ANDI) which was 16.63% and gynecomastia (11.34%). 18 cases (6.80%) were of malignant lesion. This includes 16 female and 2 male cases. The common ages for BBD were, 20-40 years for fibroadenoma, 15-40 years for breast abscess, 18-40 years for ANDI and 10-19, 50-59 for gynecomastia respectively, whereas carcinoma breast was common in the age group of forties and fifties.

CONCLUSION

We conclude from this study that BBD were the most frequent breast lesion. Among the BBD fibroadenoma was the commonest lesion. Breast carcinoma cases were less frequent and reached to the hospital in very late stage of the disease.

Inter- and intraspecies variations of the 16S-23S rDNA intergenic spacer region of various streptococcal species

The 16S-23S rDNA intergenic spacer regions (ISR) of different streptococcal species and subspecies were amplified with primers derived from the highly conserved flanking regions of the 16S rRNA and 23S rRNA genes. The single sized amplicons showed a uniform pattern for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. uberis, S. parauberis, S. pyogenes and S. equi subsp. equi, respectively. The amplicons of S. equi subsp. zooepidemicus, S. porcinus and S. suis appeared with 3, 5 and 3 different sizes, respectively. ISR of selected strains of each species or subspecies investigated were sequenced and multiple aligned. This allowed a separation of ISR into regions, with 7 regions for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. pyogenes and S. suis, 8 regions for S. uberis and S. parauberis and mostly 9 regions for S. equi subsp. equi, S. equi subsp. zooepidemicus and S. porcinus. Region 4, encoding the transfer RNA for alanine (tRNA(Ala)), was present and identical for all isolates investigated. The size and sequence of ISR appears to be a unique marker for streptococci of various species and subspecies and could be used for bacterial identification. In addition the size and sequence variations of ISR of S. equi subsp. zooepidemicus, S. porcinus and S. suis allows a molecular typing of isolates of these species possibly useful in epidemiological aspects.

Development of PCR assays for detection of Streptococcus canis

Streptococcus canis isolates, also including S. canis of artificially contaminated milk, could be identified by polymerase chain reaction (PCR) amplification using oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene and, after sequencing, according to S. canis-specific parts of the 16S-23S rDNA intergenic spacer region and with oligonucleotide primers detecting an internal fragment of the group G streptococcal CAMP factor gene cfg. The 16S rRNA gene- and CAMP factor gene cfg-specific oligonucleotide primers could be used together in a multiplex PCR. No cross-reactivities could be observed with other group G streptococcal isolates or with any of the other control strains of various streptococcal species and serogroups. The PCR methods presented in this study allowed a rapid and reliable identification of S. canis and might help to improve the diagnosis of this bacterial species in animal and human infections.

Atypical squamous cells of undetermined significance: is it worthwhile to qualify them further?

BACKGROUND

In Bethesda System of reporting cervico-vaginal smears, the equivocal epithelial cell abnormalities have been categorised as "atypical squamous and glandular cells of undetermined significance" (ASCUS and AGUS). These abnormalities may harbour minor lesions attributed to mere inflammatory changes to potentially serious high grade lesions. It is recommended to further qualify these lesions according to whether they favor a reactive or a neoplastic outcome.

AIMS

We undertook the present study to assess the significance of ASCUS qualifiers.

MATERIAL AND METHODS

A total of 12071 women were screened for early detection of cancer cervix. The women with ASCUS diagnosis were further qualified as ASCUS favor reactive and ASCUS favor SIL (Squamous intraepithelial lesion) according the Bethesda 1991 system of reporting. ASCUS-reactive cases were followed up by a repeat smear examination and persistent ASCUS cases were taken up for colposcopy and biopsy if indicated. All ASCUS-SIL cases were taken up for immediate colposcopy.

RESULTS

The pick up rate of high grade lesions was not significantly different (P=0.47; Chi square test) on the follow up of ASCUS-reactive (2/222) and ASCUS-SIL (2/130) groups. The low grade lesions were picked up in 10/222 ASCUS-reactive and 58/130 in ASCUS-SIL, which was statistically significant (P < 0.001).

CONCLUSIONS

The results of our study indicate that it is not worthwhile to qualify these lesions as majority of ASCUS-SIL also revealed only low grade epithelial which have a benign biological behaviour.

Protein kinase A RI beta subunit deficiency in lupus T lymphocytes: bypassing a block in RI beta translation reconstitutes protein kinase A activity and augments IL-2 production

A profound deficiency of type I protein kinase A (PKA-I or RIalpha/beta2C2) phosphotransferase activity occurs in the T lymphocytes of 80% of subjects with systemic lupus erythematosus (SLE), an autoimmune disorder of unknown etiology. This isozyme deficiency is predominantly the product of reduced or absent beta isoform of the type I regulatory subunit (RIbeta). Transient transfection of RIbeta cDNAs from SLE subjects into autologous T cells that do not synthesize the RIbeta subunit bypassed the block, resulting in RIbeta subunit synthesis and restoration of the PKA-Ibeta (RIbeta2C2) holoenzyme. Transfected T cells activated via the T cell surface receptor complex revealed a significant increase of cAMP-activatable PKA activity that was associated with a significant increase in IL-2 production. These data demonstrate that a disorder of RIbeta translation exists, and that correction of the PKA-I deficiency may enhance T lymphocyte effector functions in SLE.

Evaluation of PCR methods for rapid identification and differentiation of Streptococcus uberis and Streptococcus parauberis

Streptococcus uberis and Streptococcus parauberis reference strains and isolates obtained from routine diagnostics were investigated by PCR with oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene, the 23S rRNA gene, and the 16S-23S rRNA intergenic spacer region of both species. All three primer pairs allowed an identification of 67 isolates as S. uberis and 4 isolates as S. parauberis.

The effect of elevation on digital blood pressure

Elevation of the hand is recommended for all patients undergoing hand surgery to decrease the swelling in the hand. This study was designed to look at the effects of elevation of the hand on digital blood pressure at different elevation positions. Digital blood pressure was recorded using a digital plethysmograph in 30 subjects for increasing levels of elevation above the heart. Friedman's test was applied to the blood-pressure changes recorded in the four positions of the upper limb and showed a significant sustained fall in mean blood pressure with increasing elevation, bringing into question the use of elevation in certain clinical situations.

Association of deficient type II protein kinase A activity with aberrant nuclear translocation of the RII beta subunit in systemic lupus erythematosus T lymphocytes

Systemic lupus erythematosus (SLE) is an autoimmune disorder of indeterminate etiology characterized by abnormal T cell signal transduction and altered T cell effector functions. We have previously observed a profound deficiency of total protein kinase A (PKA) phosphotransferase activity in SLE T cells. Here we examined whether reduced total PKA activity in SLE T cells is in part the result of deficient type II PKA (PKA-II) isozyme activity. The mean PKA-II activity in SLE T cells was 61% of normal control T cells. The prevalence of deficient PKA-II activity in 35 SLE subjects was 37%. Deficient isozyme activity was persistent over time and was unrelated to SLE disease activity. Reduced PKA-II activity was associated with spontaneous dissociation of the cytosolic RIIbeta2C2 holoenzyme and translocation of the regulatory (RIIbeta) subunit from the cytosol to the nucleus. Confocal immunofluorescence microscopy revealed that the RIIbeta subunit was present in approximately 60% of SLE T cell nuclei compared with only 2-3% of normal and disease controls. Quantification of nuclear RIIbeta subunit protein content by immunoprecipitation and immunoblotting demonstrated a 54% increase over normal T cell nuclei. Moreover, the RIIbeta subunit was retained in SLE T cell nuclei, failed to relocate to the cytosol, and was associated with a persistent deficiency of PKA-II activity. In conclusion, we describe a novel mechanism of deficient PKA-II isozyme activity due to aberrant nuclear translocation of the RIIbeta subunit and its retention in the nucleus in SLE T cells. Deficient PKA-II activity may contribute to impaired signaling in SLE T cells.

Frequent amplification of C-erbB2 (HER-2/Neu) oncogene in cervical carcinoma as detected by non-fluorescence in situ hybridization technique on paraffin sections

Sixty primary untreated squamous cell carcinomas were studied for C-erbB2 gene amplification by non-fluorescence in situ hybridization technique. Amplified tumour cells showed intranuclear dark brown, often paired signals under light microscopy. Twenty-two out of 60 tumours (36.6%) showed signs of amplification of different degree (+ to +). Considerable heterogeneity of C-erbB2 amplification per cell was seen within each amplified tumour. The proportion of amplified cells ranged between 10 and 90% in these tumours. The arrangement of C-erbB2 in clusters in most amplified tumours suggests that C-erbB2 amplification occurs intrachromosomally. No significant difference in the frequency of amplification was observed according to clinical stage or the histological patterns of the tumours. The results of the present study showed frequent amplification of C-erbB2 in cervical carcinoma on paraffin sections. This technique was found to be more sensitive than the Southern blot technique which could detect amplification in 14% of the tumours of the same cohort.

Presence of interleukin 10 in the serum and blister fluid of patients with pemphigus vulgaris and pemphigoid

Interleukin 10 (IL-10) is an immunoregulatory cytokine produced by T lymphocytes and macrophages. Recently, it has been suggested that IL-10 may be involved in the pathogenesis of various inflammatory and autoimmune diseases. Using an ELISA we investigated the presence of IL-10 in the serum and blister fluid of pemphigus vulgaris (PV) patients with active disease and those in prolonged clinical remission compared with normal controls. Sera from patients with bullous pemphigoid (BP), ocular cicatricial pemphigoid (OCP), oral pemphigoid (OP) and blister fluid from five patients with BP were also studied. Increased levels of IL-10 were detected in the sera of 87.5% of patients with active PV and were statistically significant (P=0.0003) when compared with levels in normal human serum. Lower levels of IL-10 were detected in 12.5% PV patients in remission and were statistically significant (P=0.0001) when compared with levels in patients with active disease. Levels of IL-10 were detected in sera of 4.6% (1 of 24) of the normal controls. The levels of IL-10 were approximately four times higher in blister fluids than levels in the serum in the same PV patients. This difference was highly statistically significant (P=0.0008). A correlation was observed between serum levels of IL-10 and titres of pemphigus autoantibodies and with disease severity. Elevated level of IL-10 was detected in the blister fluid from five BP patients. Levels of IL-10 in the sera of patients with BP, OCP and OP were not significantly increased. These preliminary data suggest that IL-10 in concert with other cytokines may play an important role in the pathogenesis of PV and BP.

Diminished levels of protein kinase A RI alpha and RI beta transcripts and proteins in systemic lupus erythematosus T lymphocytes

Deficient type I protein kinase A phosphotransferase activity occurs in the T cells of 80% of subjects with systemic lupus erythematosus (SLE). To investigate the mechanism of this deficient isozyme activity, we hypothesized that reduced amounts of type I regulatory (RI) isoform transcripts, RIalpha and RIbeta, may be associated with a diminution of RIalpha and/or RIbeta protein. Sixteen SLE subjects with a mean (+/-1 SD) SLE disease activity index of 12.4 +/- 7.2 were studied. Controls included 16 normal subjects, six subjects with primary Sjögren's syndrome (SS), and three subjects with SS/SLE overlap. RT-PCR revealed that normal, SS, SS/SLE, and SLE T cells expressed mRNAs for all seven R and catalytic (C) subunit isoforms. Quantification of mRNAs by competitive PCR revealed that the ratio of RIalpha mRNA to RIbeta mRNA in normal T cells was 3.4:1. In SLE T cells there were 20 and 49% decreases in RIalpha and RIbeta mRNAs (RIbeta; p = 0.008), respectively, resulting in an RIalpha:RIbeta mRNA of 5.3:1. SS/SLE T cells showed a 72.5% decrease in RIbeta mRNA compared with normal controls (p = 0.01). Immunoblotting of normal T cell RIalpha and RIbeta proteins revealed a ratio of RIalpha:RIbeta of 3.2:1. In SLE T cells, there was a 30% decrease in RIalpha protein (p = 0.002) and a 65% decrease in RIbeta protein (p < 0.001), shifting the ratio of RIalpha:RIbeta protein to 6.5:1. T cells from 25% of SLE subjects lacked any detectable RIbeta protein. Analysis of several lupus T cell lines demonstrated a persistent deficiency of both proteins, excluding a potential effect of disease activity. In conclusion, reduced expression of RIalpha and RIbeta transcripts is associated with a decrement in RIalpha and RIbeta proteins and may contribute to deficient type I protein kinase A isozyme activity in SLE T cells.

Linear IgA bullous dermatosis in a patient with chronic renal failure: response to intravenous immunoglobulin therapy

Linear IgA bullous dermatosis is a blistering disease with a heterogeneous clinical manifestation, characterized by deposition of IgA along the basement membrane zone of perilesional skin on direct immunofluorescence. We describe a patient with chronic renal failure who experienced linear IgA bullous dermatosis. Long-term administration of intravenous immunoglobulin therapy was associated with clinical remission lasting more than 12 months.

Protein kinase A-catalyzed phosphorylation of heat shock protein 60 chaperone regulates its attachment to histone 2B in the T lymphocyte plasma membrane

Accumulating evidence suggests that the mitochondrial molecular chaperone heat shock protein 60 (hsp60) also can localize in extramitochondrial sites. However, direct evidence that hsp60 functions as a chaperone outside of mitochondria is presently lacking. A 60-kDa protein that is present in the plasma membrane of a human leukemic CD4(+) CEM-SS T cell line and is phosphorylated by protein kinase A (PKA) was identified as hsp60. An 18-kDa plasma membrane-associated protein coimmunoprecipitated with hsp60 and was identified as histone 2B (H2B). Hsp60 physically associated with H2B when both molecules were in their dephospho forms. By contrast, PKA-catalyzed phosphorylation of both hsp60 and H2B caused dissociation of H2B from hsp60 and loss of H2B from the plasma membrane of intact T cells. These results suggest that (i) hsp60 and H2B can localize in the T cell plasma membrane; (ii) hsp60 functions as a molecular chaperone for H2B; and (iii) PKA-catalyzed phosphorylation of both hsp60 and H2B appears to regulate the attachment of H2B to hsp60. We propose a model in which phosphorylation/dephosphorylation regulates chaperoning of H2B by hsp60 in the plasma membrane.

Marginal vacuoles in thyroid aspirates

OBJECTIVES

To report on two cases of metastatic follicular carcinoma with marginal vacuoles (MVs) and review smear results in 441 solitary nodular goiters (SNGs) for this cytologic feature.

STUDY DESIGN

The first case was a 55-year-old male who presented with a huge mass in the left hip region; the second case was a 50-year-old male with a thyroid nodule and a large mass on the scalp. The age of the 441 ultrasonographically diagnosed SNG cases ranged from 11 to 75 years. The May-Grünwald-Giemsa-stained fine needle aspiration (FNA) smears of these cases were reviewed by one of the authors (D.K.D.) for various cytomorphologic features, including MVs.

RESULTS

FNA smears from the mass in the hip in the first case showed follicular cells with acinar formation and MVs, indicating metastatic follicular thyroid carcinoma (FTC). These features were of help in detecting the thyroid primary, which had previously gone undetected. Aspiration smears from the thyroid nodule and the mass on the scalp in the second case showed tumor cells of FTC with MVs and microfilariae. Review of 441 SNG cases revealed MVs in 42.6% of hyperplastic nodules; that rate was significantly higher (P < .001) than that of colloid goiter (5.2%) and neoplastic goiter (13.3%) but lower (P < .05) than that of thyrotoxic goiter (100%). MVs were limited to neoplasms with a follicular component; that included 15% of follicular neoplasms and 50% of follicular variant of papillary carcinoma (FVPC). The difference between FVPC and the rest of the neoplastic goiters (6%) was statistically significant (P = .002).

The scarring processes in mucosal tissues after immune injury

OBJECTIVES

An important feature of the healing processes is scar formation which may be necessary for organism survival. If it proceeds to the pathological state, it may impair normal function. The purpose of this review is to focus on some of the factors that may influence this process after immune injury, comparing it in the skin and mucosa.

METHODS

A detailed literature search of peer-reviewed journals was conducted. Studies reported in all languages considered relevant and important were used, including humans, animals, and tissue culture.

RESULTS

Analysis of the data indicate that the scarring process is mainly dependent on (1) the type of the lesion, (2) the cause and duration of injury, and (3) the tissue involved and its microenvironment. Equally important is the large spectrum and heterogenicity in the biological activity of fibroblasts and their role in scar formation.

CONCLUSIONS

The process of scar formation is complex and multistep process and is affected and influenced by local and systemic factors. Although it appears irreversible, there are pharmacological agents available, and under investigation, that may minimize its detrimental effects.

Deficient type I protein kinase A isozyme activity in systemic lupus erythematosus T lymphocytes: II. Abnormal isozyme kinetics

Systemic lupus erythematosus (SLE) T cells exhibit deficient type I protein kinase A (PKA-1) isozyme phosphotransferase activity, resulting in impaired phosphorylation of plasma membrane-associated proteins. To determine the mechanism of this isozyme deficiency, we studied 16 SLE subjects with a mean (+/-1 SD) SLE disease activity index of 16.7 +/- 8.8 and 16 normal controls. Immunoblotting of type I regulatory (RI) subunit protein in SLE and control T cells demonstrated no significant differences in the amount of protein. Analysis of isozyme kinetics in SLE T cells demonstrated a 2.2-fold increase in the Michaelis-Menten constant, a 2.5-fold increase in the apparent association constant for cAMP, a 3.8-fold decrease in the maximal velocity, and a reduction in the mean maximal binding of cAMP to the RI subunit compared with control T cells. Reduction of the Hill coefficient from 1.2 in normal T cells to 0.7 in SLE T cells indicated a loss of positive cooperativity between cAMP binding sites A and B. An increase in the apparent association constant for cAMP signifies relative resistance to cAMP, indicating that higher intracellular concentrations of cAMP are necessary to activate the isozyme. Because the R subunit of PKA is the only intracellular receptor for cAMP, the abnormal isozyme kinetics may account for the deficiency of PKA-I phosphotransferase activity and impaired PKA-I-catalyzed protein phosphorylation observed in SLE T cells. This disordered isozyme function may contribute to the altered signal transduction and observed cellular immune dysfunctions in SLE. Moreover, these altered isozyme kinetics raise the possibility of a structural defect(s) in the RI subunit.

Deficient type I protein kinase A isozyme activity in systemic lupus erythematosus T lymphocytes: II. Abnormal isozyme kinetics

Systemic lupus erythematosus (SLE) T cells exhibit deficient type I protein kinase A (PKA-1) isozyme phosphotransferase activity, resulting in impaired phosphorylation of plasma membrane-associated proteins. To determine the mechanism of this isozyme deficiency, we studied 16 SLE subjects with a mean (+/-1 SD) SLE disease activity index of 16.7 +/- 8.8 and 16 normal controls. Immunoblotting of type I regulatory (RI) subunit protein in SLE and control T cells demonstrated no significant differences in the amount of protein. Analysis of isozyme kinetics in SLE T cells demonstrated a 2.2-fold increase in the Michaelis-Menten constant, a 2.5-fold increase in the apparent association constant for cAMP, a 3.8-fold decrease in the maximal velocity, and a reduction in the mean maximal binding of cAMP to the RI subunit compared with control T cells. Reduction of the Hill coefficient from 1.2 in normal T cells to 0.7 in SLE T cells indicated a loss of positive cooperativity between cAMP binding sites A and B. An increase in the apparent association constant for cAMP signifies relative resistance to cAMP, indicating that higher intracellular concentrations of cAMP are necessary to activate the isozyme. Because the R subunit of PKA is the only intracellular receptor for cAMP, the abnormal isozyme kinetics may account for the deficiency of PKA-I phosphotransferase activity and impaired PKA-I-catalyzed protein phosphorylation observed in SLE T cells. This disordered isozyme function may contribute to the altered signal transduction and observed cellular immune dysfunctions in SLE. Moreover, these altered isozyme kinetics raise the possibility of a structural defect(s) in the RI subunit.

Deficient type I protein kinase A isozyme activity in systemic lupus erythematosus T lymphocytes

Systemic lupus erythematosus (SLE) is an autoimmune disorder of indeterminate etiology characterized by a dysfunctional cellular immune response. We have previously identified a metabolic disorder of the adenylate cyclase/cAMP/protein kinase A (AC/cAMP/PKA) pathway characterized by impaired cAMP-inducible, PKA-catalyzed protein phosphorylation in intact T lymphocytes from subjects with severe SLE disease activity. Because this metabolic disorder may contribute to abnormal T cell immune effector functions, we tested the hypothesis that impaired PKA-dependent protein phosphorylation is the result of a PKA isozyme deficiency in SLE T lymphocytes. Compared with healthy and rheumatoid arthritis (RA) controls, subjects with severe SLE activity exhibited reduced PKA-catalyzed phosphorylation of proteins in the T lymphocyte plasma membrane where the type I isozyme of PKA (PKA-I) is predominantly localized. Both silver staining and biosynthetic labeling of membrane-associated proteins with [35S]methionine demonstrated that reduced protein phosphorylation was not due to either an altered distribution of or absence of proteins. Moreover, phosphorylation of SLE membrane-associated proteins with the PKA catalytic (C) subunit showed a similar distribution and extent of phosphorylation compared with membrane proteins from healthy T cells, suggesting that SLE T cell membrane proteins could be phosphorylated. Sequential column chromatography of the type I and type II isozymes of PKA (PKA-I, PKA-II) demonstrated a deficiency of PKA-I isozyme activity. Compared with a ratio of PKA-I to PKA-II activity of 4.2:1 in healthy T cells, the activity ratio in T cells from subjects with severe SLE disease activity was 0.99:1 (P = 0.01, SLE versus healthy controls for PKA-I). The deficient PKA-I activity was associated with a significant increase of free C-subunit activity (P = 0.04, SLE versus healthy controls for C-subunit). T cells from subjects with mild/moderate SLE disease activity also exhibited diminished PKA-I activity, yielding a ratio of PKA-I to PKA-II activity of 2.4:1. By contrast, T cells from RA controls possessed increased PKA-I, PKA-II, and free C-subunit activities compared with healthy controls, resulting in a ratio of PKA-I to PKA-II activity of 3.6:1. We conclude that the reduced PKA-catalyzed protein phosphorylation in the plasma membrane of SLE T cells is the result of deficient PKA-I isozyme activity. This is the first identification of a deficiency of PKA activity in SLE T lymphocytes; the deficiency, resulting in diminished protein phosphorylation, may alter cellular homeostasis, contributing to the cellular immune dysfunctions observed in SLE.

Chemical carcinogens increase IL-1 alpha and IL-6 gene transcripts in human keratinocytes

Using reverse transcriptase-linked polymerase chain reaction, the effect of polycyclic aromatic hydrocarbons (PAHs) on IL-1 alpha, IL-1 beta and IL-6 gene expression in cultured human keratinocytes was studied. Exposure to beta-naphthoflavone and benz(a)anthracene resulted in a higher copy number of IL-1 alpha and IL-6 mRNA while lower level of IL-1 beta mRNA was detected in these cells. These data suggest that, like ultraviolet B (UVB) radiation, ubiquitous environmental carcinogenic PAHs are potent inducers of IL-1 alpha and IL-6 cytokines and, unlike UVB, they downregulate IL-1 beta in human keratinocytes.

Modulation of interferon-gamma-induced HLA-DR expression on the human keratinocyte cell line SCC-13 by ultraviolet radiation

Cell surface expression of major histocompatibility determinants on epidermal keratinocytes is a characteristic feature of a number of inflammatory dermatoses and in all likelihood is caused by diffusion of human leukocyte antigen (HLA)-DR-inducing cytokines from cells present in the dermal mononuclear cell infiltrate. Many of these same disorders respond to ultraviolet (UV) radiation phototherapy. Using the human SCC-13 keratinocyte cell line as a model, UV radiation was found to inhibit interferon-gamma-induced HLA-DR expression. Inhibition correlated closely with decreased steady-state levels of HLA-DR mRNA. These findings provide evidence that the therapeutic effect of UV radiation phototherapy may be mediated by its capacity to down-regulate cytokine-induced keratinocyte HLA-DR expression.

Pilomatricoma: a retrospective study

A study of 53 Pakistani patients with pilomatricoma diagnosed at AFIP during 1985-1989 is presented. It constituted 37.2% of all benign adnexal tumors, during the same period. 56.2% of patients were more than 30 years of age. Differences in site, sex, and age distribution from Western reports were observed. Unusual clinical presentations were also noted. This study outlines the clinicopathologic features of pilomatricoma in Pakistan.

Induction of CYP1A1 mRNA in rat epidermis and cultured human epidermal keratinocytes by benz(a)anthracene and beta-naphthoflavone

Cytochrome P-4501A1 (CYP1A1) plays a major role in the bioactivation of procarcinogens in target tissues, including skin. However, the factors controlling CYP1A1 expression in mammalian skin are unknown. Utilizing the reverse transcriptase-linked polymerase chain reaction, we analyzed the effect of treatment with beta-naphthoflavone (beta-NF) and benz(a)anthracene on the expression of CYP1A1 mRNA in rat epidermis and normal human epidermal keratinocytes (NHEK). Inducer treatment of rats and NHEKs resulted in several-fold increases in aryl hydrocarbon hydroxylase activity. Following inducer treatment of adult or neonatal rats, increase in CYP1A1 gene message occurred as compared with that in controls. Higher basal level and inducibility were detected in mature rather than in 4-day-old rats. This induction occurred as early as 4 hr after beta-NF application. Exposure to beta-NF and benz(a)anthracene also resulted in substantial increases in gene message in NHEK. Northern blot analyses complemented the polymerase chain reaction data. These results indicate that CYP1A1 gene expression is increased in mammalian epidermis by inducers of epidermal aryl hydrocarbon hydroxylase activity.

Colloid carcinoma of the breast with concomitant metastasis and a tuberculous lesion in the axillary lymph nodes. A case report

A 30-year-old woman presented with a lump in the left breast and left axillary lymphadenopathy that, on fine needle aspiration cytology (FNAC), proved to be duct cell carcinoma with metastasis. Histology of the radical mastectomy specimen showed a mixed colloid carcinoma. Axillary lymph nodes revealed a variety of pathologic changes consisting of reactive hyperplasia, tuberculosis and metastasis. A combination of a tuberculous lesion and metastasis in the same lymph nodes was also found. During follow-up, after radiotherapy, the patient developed left supraclavicular and right cervical lymphadenopathy that, on FNAC, revealed a tuberculous lesion and metastasis, respectively. The rarity of this condition with double pathology is highlighted, and the reason behind the limitations of FNA in subtyping the primary malignancy and its failure to detect the tuberculous lesion in the axillary lymph node are discussed.

Metabolism of benzo[a]pyrene by human melanocytes in culture

Benzo[a]pyrene (B[a]P) is a ubiquitous environmental pollutant and known skin carcinogen. In the present study, in vitro addition of [3H]B[a]P to normal human melanocytes in culture, isolated from adult human skin, resulted in the metabolism of [3H]B[a]P both intracellularly and extracellularly. HPLC analysis showed that [3H]B[a]P-9,10- and 7,8-diol were the major intracellular and extracellular metabolites followed by 3,6-quinone, 9-hydroxy and 3-hydroxy metabolites. Significant amounts of the [3H]B[a]P metabolites were found to be present in the sonicated cell suspension and culture medium as the glucuronide and sulfate conjugates. In total 37.3% of the [3H]B[a]P added in the culture medium was metabolized by melanocytes, of which 21.1% was quantified as the intracellular and 16.2% as the extracellular metabolites. Our data show that human melanocytes are capable of metabolizing B[a]P.