Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of oral bioavailability enhancing formulations during drug discovery

The objective of this paper was to identify oral bioavailability enhancing approaches for a poorly water-soluble research compound during drug discovery stages using minimal amounts of material. LCQ789 is a pBCS (preclinical BCS) Class II compound with extremely low aqueous solubility (<1 µg/mL) and high permeability, therefore, resulting in very low oral bioavailability in preclinical species (rats and dogs). A number of solubility and/or dissolution enhancing approaches including particle size reduction, solid dispersions, lipid-based formulations and co-crystals, were considered in order to improve the compound’s oral bioavailability. High-Throughput Screening (HTS) and in silico modeling (GastroPlus™) were utilized to minimize the compound consumption in early discovery stages. In vivo evaluation of selected physical form and formulation strategies was performed in rats and dogs. Amongst the formulation strategies, optimized solid dispersion and lipid-based formulation provided significant improvement in drug dissolution rate and hence, oral bioavailability. In addition, a significant impact of physical form on oral bioavailability of LCQ789 was observed. In conclusion, a thorough understanding of not only the formulation technique but also the physical form of research compounds is critical to ensure physical stability, successful pharmacokinetic (PK) profiling and early developability risk assessment.
Estrategias de diferenciación en Internet

La "tienda virtual" presenta los mismos retos que cualquier otro tipo de distribucion comercial, como son atraer hacia ella a los potenciales clientes y que, una vez alli compren. Este articulo se centra en como marcar tambien la diferencia en el mercado virtual.
Novel Miniature Transposable Elements in Thermophilic Synechococcus Strains and Their Impact on an Environmental Population

ABSTRACT The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B′a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, resulting in an overall high abundance of insertion sequences in the genomes. In addition to full-length copies, a large number of internal deletion variants have been identified. ISSoc2 has two variants (ISSoc2∂-1 and ISSoc2∂-2) that are observed to have multiple near-exact copies. Comparison of environmental metagenomic sequences to the Synechococcus genomes reveals novel placement of copies of ISSoc2, ISSoc2∂-1, and ISSoc2∂-2. Thus, ISSoc2∂-1 and ISSoc2∂-2 appear to be active nonautonomous mobile elements derived by internal deletion from ISSoc2. Insertion sites interrupting genes that are likely critical for cell viability were detected; however, most insertions either were intergenic or were within genes of unknown function. Most novel insertions detected in the metagenome were rare, suggesting a stringent selective environment. Evidence for mobility of internal deletion variants of other insertion sequences in these isolates suggests that this is a general mechanism for the formation of miniature insertion sequences.
Diagnostic Capability of Next-Generation Sequencing Fusion Analysis in Identifying a Rare CASE of TRAF1-ALK-Associated Anaplastic Large Cell Lymphoma

Background: Anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma (ALCL) is a rare T-cell neoplasm, accounting for approximately 3% of adult non-Hodgkin lymphomas. Although NPM1 is the most common fusion partner with ALK, many others have been described, necessitating break-apart FISH studies for confirmation of the diagnosis. TNF receptor-associated factor 1 (TRAF1) is a rare ALK partner that is thought to confer a worse prognosis in patients. We describe the utility of next-generation sequencing (NGS) RNA analysis in detection of this uncommon ALK partner. Case Description: A 42-year-old male with cervical lymphadenopathy presented for excisional biopsy. Following a tissue diagnosis of ALCL, ALK+, RNA from the biopsy was extracted from Formalin-fixed paraffin-embedded (FFPE) tissue and prepared for Anchored Multiplex PCR using the Archer® FusionPlex® v2 assay, which employs unidirectional gene-specific primers using NGS to detect novel or unknown gene partners. Results: Histologic evaluation of the excised lymph node showed atypical cells, including “horseshoe/kidney”-shaped nuclei. Neoplastic cells were immunoreactive against CD30, ALK (diffuse, cytoplasmic), CD2, CD4, granzyme B, and TIA-1. A diagnosis of ALCL, ALK+ was made. The pattern of ALK immunostaining suggested a non-NPM1-associated ALK translocation pattern, prompting further investigation. NGS fusion analysis showed a translocation involving exon 7 of TRAF1 and exon 20 of ALK. Conclusion: ALK positivity suggests an overall favorable prognosis of ALCL as compared to ALK-negative cases. However, in the rare published cases of TRAF1-ALK, an aggressive clinical course has been observed, which may reflect the aggressive propensity of this particular fusion, as these cases appear to be refractory to standard chemotherapy and also to the first generation ALK inhibitors. This study highlights the advantage of using NGS in RNA-based fusion assays to detect rare translocations, which can be of some clinical importance in detecting rare but aggressive fusion partners of ALK. As these technologies become more available, there is potential to identify such changes and effectively stratify the prognosis of ALCL patients.
Effect of short-term hyperglycemia on adipose tissue fluxes of selected cytokines in vivo during multiple phases of diet-induced weight loss in obese women.

CONTEXT Hyperglycemia is suggested to be one of the drivers of the proinflammatory state observed in obese and diabetic patients. OBJECTIVES The objectives of the study was to investigate whether sc abdominal adipose tissue (scAT) could be one of the important sources of proinflammatory cytokines released in response to short-term hyperglycemia and whether this secretion capacity could be influenced by weight loss. DESIGN, PATIENTS, AND INTERVENTIONS Output of cytokines and proteins of acute phase from scAT in response to a 3-hours hyperglycemic clamp was evaluated in nine obese women in vivo using Fick's principle. Moreover, the output of cytokines was analyzed during a multiphase dietary intervention consisting of 1 month on a very low-calorie diet and subsequent 5-month weight-stabilization phase. MAIN OUTCOME MEASURE(S) The levels of cytokines and proteins of acute phase [IL-6, IL-8, IL-1 receptor antagonist (IL-1Ra), TNF-α, monocyte chemoattractant protein-1 (MCP-1), serum amyloid A, and C-reactive protein] in arterial and venous plasma were measured during each dietary phase. The insulin sensitivity of scAT in respect to the antilipolytic effect of insulin during the clamp was assessed. RESULTS Hyperglycemia increased the output of cytokines IL-6, MCP-1, and IL-1Ra from scAT. This effect had a tendency to be reduced after weight loss. The output of other proinflammatory substances from scAT into circulation was not detected. The diet-induced weight loss was associated with the improvement of antilipolytic insulin sensitivity in scAT. CONCLUSIONS The results suggest that short-term hyperglycemia induces an increase of the output of cytokines IL-6, IL-1Ra, and MCP-1 from adipose tissue, and this deleterious hyperglycemia effect may be attenuated by the diet-induced weight reduction. This lowered responsiveness of the inflammation-related system may be an important feature of the weight reduction-induced improvement of the metabolic status of obese prediabetic individuals.
The Heparin/Heparan Sulfate Sequence That Interacts with Cyclophilin B Contains a 3-O-Sulfated N-Unsubstituted Glucosamine Residue*

Many of the biological functions of heparan sulfate (HS) proteoglycans can be attributed to specialized structures within HS moieties, which are thought to modulate binding and function of various effector proteins. Cyclophilin B (CyPB), which was initially identified as a cyclosporin A-binding protein, triggers migration and integrin-mediated adhesion of peripheral blood T lymphocytes by a mechanism dependent on interaction with cell surface HS. Here we determined the structural features of HS that are responsible for the specific binding of CyPB. In addition to the involvement of 2-O,6-O, and N-sulfate groups, we also demonstrated that binding of CyPB was dependent on the presence of N-unsubstituted glucosamine residues (GlcNH2), which have been reported to be precursors for sulfation by 3-O-sulfotransferases-3 (3-OST-3). Interestingly, 3-OST-3B isoform was found to be the main 3-OST isoenzyme expressed in peripheral blood T lymphocytes and Jurkat T cells. Moreover, down-regulation of the expression of 3-OST-3 by RNA interference potently reduced CyPB binding and consequent activation of p44/42 mitogen-activated protein kinases. Altogether, our results strongly support the hypothesis that 3-O-sulfation of GlcNH2 residues could be a key modification that provides specialized HS structures for CyPB binding to responsive cells. Given that 3-O-sulfation of GlcNH2-containing HS by 3-OST-3 also provides binding sites for glycoprotein gD of herpes simplex virus type I, these findings suggest an intriguing structural linkage between the HS sequences involved in CyPB binding and viral infection.
Copper Sulfide Nanoparticles-Incorporated Hyaluronic Acid Injectable Hydrogel With Enhanced Angiogenesis to Promote Wound Healing

Skin wound caused by trauma, inflammation, surgery, or burns remains a great challenge worldwide since there is no effective therapy available to improve its clinical outcomes. Herein, we report a copper sulfide nanoparticles-incorporated hyaluronic acid (CuS/HA) injectable hydrogel with enhanced angiogenesis to promote wound healing. The prepared hydrogel could not only be injected to the wound site but also exhibited good photothermal effect, with temperature increasing to 50°C from room temperature after 10 min of near-infrared light irradiation. The cell culture experiments also showed that the hydrogel has no cytotoxicity. In the rat skin wound model, the hydrogel treated wounds exhibited better healing performances. Masson’s trichrome staining suggested that collagen deposition in wounds treated with the hydrogel was significantly higher than other groups. The immunohistochemical staining showed that the hydrogel can effectively upregulate the expression of vascular endothelial growth factor (VEGF) in the wound area at the incipient stage of healing, and the CD 31 immunofluorescence staining confirmed the enhanced angiogenesis of the hydrogel. Taken together, the prepared CuS/HA hydrogel can effectively increase the collagen deposition, upregulate the expression of VEGF, and enhance the angiogenesis, which may contribute to promote wound healing, making it a promising for application in treating skin wound.
Genomic Characterization of Primary Invasive Lobular Breast Cancer.

PURPOSE Invasive lobular breast cancer (ILBC) is the second most common histologic subtype after invasive ductal breast cancer (IDBC). Despite clinical and pathologic differences, ILBC is still treated as IDBC. We aimed to identify genomic alterations in ILBC with potential clinical implications. METHODS From an initial 630 ILBC primary tumors, we interrogated oncogenic substitutions and insertions and deletions of 360 cancer genes and genome-wide copy number aberrations in 413 and 170 ILBC samples, respectively, and correlated those findings with clinicopathologic and outcome features. RESULTS Besides the high mutation frequency of CDH1 in 65% of tumors, alterations in one of the three key genes of the phosphatidylinositol 3-kinase pathway, PIK3CA, PTEN, and AKT1, were present in more than one-half of the cases. HER2 and HER3 were mutated in 5.1% and 3.6% of the tumors, with most of these mutations having a proven role in activating the human epidermal growth factor receptor/ERBB pathway. Mutations in FOXA1 and ESR1 copy number gains were detected in 9% and 25% of the samples. All these alterations were more frequent in ILBC than in IDBC. The histologic diversity of ILBC was associated with specific alterations, such as enrichment for HER2 mutations in the mixed, nonclassic, and ESR1 gains in the solid subtype. Survival analyses revealed that chromosome 1q and 11p gains showed independent prognostic value in ILBC and that HER2 and AKT1 mutations were associated with increased risk of early relapse. CONCLUSION This study demonstrates that we can now begin to individualize the treatment of ILBC, with HER2, HER3, and AKT1 mutations representing high-prevalence therapeutic targets and FOXA1 mutations and ESR1 gains deserving urgent dedicated clinical investigation, especially in the context of endocrine treatment.
AwareCare: a pilot randomized controlled trial of an awareness-based staff training intervention to improve quality of life for residents with severe dementia in long-term care settings

ABSTRACT Background: The extent to which care home residents with severe dementia show awareness is influenced by the extent to which the environment provides opportunities for engagement and by the way in which care staff interact with them. We aimed to establish whether training care staff to observe and identify signs of awareness in residents with severe dementia resulted in improved quality of life for residents. Methods: In this pilot cluster randomized trial, care staff in four homes (n = 32) received training and supervision and carried out structured observations of residents using the AwareCare measure (n = 32) over an eight-week period, while staff in four control homes (n = 33) had no training with regard to their residents (n = 33) and no contact with the research team. The primary outcome was resident quality of life. Secondary outcomes were resident well-being, behavior and cognition, staff attitudes and well-being, and care practices in the home. Results: Following intervention, residents in the intervention group had significantly better quality of life as rated by family members than those in the control group, but care staff ratings of quality of life did not differ. There were no other significant between-group differences. Staff participating in the intervention identified benefits in terms of their understanding of residents’ needs. Conclusions: Staff were able to use the observational measure effectively and relatives of residents in the intervention homes perceived an improvement in their quality of life.
Distributed Text Classification With an Ensemble Kernel-Based Learning Approach

Constructing a single text classifier that excels in any given application is a rather inviable goal. As a result, ensemble systems are becoming an important resource, since they permit the use of simpler classifiers and the integration of different knowledge in the learning process. However, many text-classification ensemble approaches have an extremely high computational burden, which poses limitations in applications in real environments. Moreover, state-of-the-art kernel-based classifiers, such as support vector machines and relevance vector machines, demand large resources when applied to large databases. Therefore, we propose the use of a new systematic distributed ensemble framework to tackle these challenges, based on a generic deployment strategy in a cluster distributed environment. We employ a combination of both task and data decomposition of the text-classification system, based on partitioning, communication, agglomeration, and mapping to define and optimize a graph of dependent tasks. Additionally, the framework includes an ensemble system where we exploit diverse patterns of errors and gain from the synergies between the ensemble classifiers. The ensemble data partitioning strategy used is shown to improve the performance of baseline state-of-the-art kernel-based machines. The experimental results show that the performance of the proposed framework outperforms standard methods both in speed and classification.
Terabit-per-square-inch data storage using phase-change media and scanning electrical nanoprobes

A theoretical study of the write, read, and erase processes in electrical scanning probe storage on phase-change media is presented. Electrical, thermal, and phase-transformation mechanisms are considered to produce a physically realistic description of this new approach to ultrahigh-density data storage. Models developed are applied to the design of a suitable storage layer stack with the necessary electrical, thermal, and tribological properties to support recorded bits of nanometric scale. The detailed structure of nanoscale crystalline and amorphous bits is also predicted. For an optimized trilayer stack comprising Ge/sub 2/Sb/sub 2/Te/sub 5/ sandwiched by amorphous or diamond-like carbon layers, crystalline bits were roughly trapezoidal in shape while amorphous bits were semi-ellipsoidal. In both cases, the energy required to write individual bits was very low (of the order of a few hundred picoJoules). Amorphous marks could be directly overwritten (erased), but crystalline bits could not. Readout performance was investigated by calculating the readout current as the tip scanned over isolated bits and bit patterns of increasing density. The highest readout contrast was generated by isolated crystalline bits in an amorphous matrix, but the narrowest readout pulses arose from isolated amorphous marks in a crystalline background. To assess the ultimate density capability of electrical probe recording the role of write-induced intersymbol interference and the thermodynamic stability of nanoscale marks were also studied.
Specific DNA binding of Stat5, but not of glucocorticoid receptor, is required for their functional cooperation in the regulation of gene transcription

Prolactin and glucocorticoid hormone are signals which regulate the transcription of milk protein genes in mammary epithelial cells. We have investigated the molecular mechanisms by which these hormones cooperate in the induction of transcription. Both hormones activate latent transcription factors in the cytoplasm of mammary epithelial cells. Prolactin exerts its effect through binding to the extracellular domain of the prolactin receptor and through receptor dimerization. This leads to the activation of a protein tyrosine kinase (Jak2), which is noncovalently associated with the cytoplasmic domain of the prolactin receptor. Jak2 phosphorylates the signal transducer and transcription activator (Stat5) which causes its dimerization and nuclear translocation where Stat5 specifically binds to sequence elements in the promoter regions of milk protein genes. In comparison, the glucocorticoid receptor is activated by a lipophilic steroid ligand in the cytoplasm which causes allosteric changes in the molecule, dimerization, and nuclear localization. It has been demonstrated that Stat5 and the glucocorticoid receptor form a molecular complex which cooperates in the induction of transcription of the beta-casein gene. We have defined the DNA sequence requirements for this cooperative mechanism and have delimited the functional domains in Stat5 and the glucocorticoid receptor that are necessary for the functional interaction. We find that the Stat5 response element (Stat5RE) within the beta-casein gene promoter is sufficient to elicit the cooperative action of Stat5 and the glucocorticoid receptor on transcription. Activation of Stat5 through phosphorylation of tyrosine 694 is an absolute prerequisite for transcription. Deletion of the transactivation domain of Stat5 results in a molecule which cannot mediate transactivation by itself but can still cooperate with the glucocorticoid receptor. Mutated variants of the glucocorticoid receptor with a nonfunctional DNA binding domain or a DNA binding domain contributed by the estrogen receptor are still able to cooperate with Stat5 in transcriptional induction. Deletion of the ligand binding domain of the glucocorticoid receptor does not impede cooperation with Stat5, whereas deletion of the AF-1 transactivation domain does prevent cooperation. Our results indicate that the glucocorticoid receptor acts as a ligand-dependent coactivator of Stat5 independently of its DNA binding function.
MicroRNA‐125b suppresses the development of bladder cancer by targeting E2F3

Increasing evidence has suggested that dysregulation of certain microRNAs (miRNAs) may contribute to tumorigenesis. microRNA‐125b (miR‐125b) was implicated to have close relationship with cell proliferation and differentiation, and downregulation of miR‐125b was observed in various types of cancers. However, the biological function of miR‐125b in bladder tumorigenesis is still unknown. In our study, we showed that the expression of miR‐125b was significantly decreased in bladder cancer tissues and four bladder cancer cell lines. Moreover, miR‐125b could suppress bladder cancer cells to form colonies in vitro and to develop tumors in nude mice. E2F3, which was critical for G1/S transition and was overexpressed in most of poor‐differentiated bladder cancers, was identified as a target of miR‐125b by luciferase assay. The E2F3 mRNA and protein expression levels were detected in bladder cancer tissues and cell lines, and interestingly, inverse correlations between miR‐125b and E2F3 protein level were found in bladder cancer tissues and four E2F3 nonamplified cell lines. Introduction of miR‐125b could reduce the expression of E2F3 protein but not the E2F3 mRNA. In addition, we observed that transfection of miR‐125b could inhibit the expression of Cyclin A2, one of the E2Fs‐responsive genes involved in G1/S transition. These results suggest that miR‐125b may regulate G1/S transition through the E2F3–Cyclin A2 signaling pathway. Taken together, miR‐125b may act as a tumor suppressor in bladder urothelium, and downregulation of miR‐125b may contribute to the tumorigenesis of bladder cancer.
Unusual case of metastatic neuroendocrine tumor.

OBJECTIVE To report a rare case of metastatic growth hormone (GH)-secreting pituitary carcinoma causing acromegaly. METHODS We present a case report and review the available literature on this topic. RESULTS A 68-year-old woman presented with persistent acromegaly after treatment for a GH-secreting pituitary adenoma. Evaluation of long-standing cervical adenopathy revealed findings consistent with a metastatic neuroendocrine tumor. Further work-up revealed additional thyroid, parathyroid, and cervical masses. After operative treatment including total thyroidectomy, subtotal parathyroidectomy, partial thymectomy, and right modified radical neck dissection, the patient's symptoms diminished, and her GH levels approached the normal range. Surgical pathology findings were consistent with a GH-secreting pituitary carcinoma metastatic to the cervical lymph nodes, multinodular thyroid hyperplasia with a focus of papillary microcarcinoma, and parathyroid hyperplasia. CONCLUSION Overall, pituitary carcinomas are extremely rare. To date, about 100 cases have been reported in the world's literature, and of these, only 19 cases originated from GH-secreting cells. Our examination of the symptoms, signs, diagnosis, and treatment of our patient, in comparison with the previously reported cases, should enhance awareness of this unusual disease process.