gebhart/patrepeval huggingface dataset:
Measurement of optical properties to quantify healing of chronic diabetic wounds (2006)

Measurement of scattering and absorption characteristics of tissue by near infrared spectroscopy may provide a clinically applicable, quantitative method of assessing healing of diabetic wounds. Twenty SICH-1 hairless rats were divided into a control group and a streptozotocin-induced diabetic group. Full-thickness wounds were made on the dorsal surface of each animal. Wounds were examined using a near infrared device with three wavelengths of incident light. Amplitude and phase of scattered light were obtained at four different source detector distances at each wavelength. The probe was positioned at six different locations. Tissue absorption and scattering coefficients were calculated from amplitude and phase data. Wound dimensions were calculated by cross and parallel polarization. Thirty-eight wounds were evaluated during the experiment. Wound size decreased at twice the rate in the control animals, whereas the average absorption coefficient was higher by a factor of two while the average value of the reduced scattering coefficient was 30% higher in the diabetic wounds. During healing, both scattering and absorption coefficients increased faster in the diabetics. Higher absorption in diabetic rats suggests impaired blood flow. Scattering may reflect tissue disorganization observed in delayed wound healing. We conclude that near infrared spectroscopy may differentiate between healing diabetic and nondiabetic wounds.
Tumor induction relationships in development of transplantable cancers of the colon in mice for chemotherapy assays, with a note on carcinogen structure. (1975)

In an effort to establish an animal colon tumor model suitable for biological and chemotherapy studies, 82 colon tumors were induced and transplanted in four different inbred strains of mice. Four colon tumors survived the first transplant and are now in serial passage. All are suitable for chemotherapy trials. Two tumors are highly metastatic, and at least one of these is known to be suitable for surgery-chemotherapy adjuvant studies. The effective colon carcinogens contained a (see article) molecular similarity.
Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus (2004)

Among methicillin-resistant Staphylococcus aureus isolates, a staphylococcal chromosomal cassette containing the mecA gene (SCCmec) is integrated into the chromosome at a unique site. SCCmec also contains unique ccrAB recombinase genes mediating its integration and excision from the genome and is flanked by characteristic left and right direct- and inverted-repeat sequences. A few non-mecA-containing SCC elements that have the other molecular features described above have recently been described. The origin of these cassettes is not clear. We have identified two new members of the SCC family integrated within orfX in Staphylococcus epidermidis strain ATCC 12228, neither of which carries mecA. One is a 57-kb element flanked by a unique 28-bp SCC direct repeat. It was called the SCC composite island (SCC-CI) because it carries a 19-kb SCC element (SCCpbp4) nested within it. SCCpbp4 contains pbp4 and tagF genes, as well as one pair of ccrAB genes (allotype 2) flanked by classical SCC-specific terminal repeats. External to SCCpbp4, SCC-CI contains a second pair of ccrAB genes (allotype 4), three IS431 elements, and genes mediating resistance to heavy metals. Genes mediating restriction-modification that may facilitate horizontal transfer are also present within SCC-CI, both within and outside SCCpbp4. Several novel arrangements of the SCC direct and inverted repeats were identified. Several long stretches of homology with other SCCs were found within and outside SCCpbp4. In view of the fact that SCC-CI was found in a commensal species, it may represent a reservoir for sequences involved in genetic shuffling between staphylococci and may contribute to the diversity found in SCC elements.
The Structure of Psychiatric Science (2014)

This essay addresses two interrelated questions: What is the structure of current psychiatric science and what should its goals be? The author analyzed all studies addressing the etiology of psychiatric disorders in the first four 2013 issues of 12 psychiatry and psychology journals. He classified the resulting 197 articles by the risk factors examined using five biological, four psychological, and three environmental levels. The risk factors were widely dispersed across levels, suggesting that our field is inherently multilevel and already practicing empirically based pluralism. However, over two-thirds of the studies had a within-level focus. Two cross-level patterns emerged between 1) systems neuroscience and neuropsychology and 2) molecular or latent genetic factors and environmental risks. The author suggests three fundamental goals for etiological psychiatric research. The first is an eclectic effort to clarify risk factors regardless of level, including those assessed using imaginative understanding, with careful attention to causal inference. An interventionist framework focusing on isolating causal effects is recommended for this effort. The second goal is to clarify mechanisms of illness that will require tracing causal pathways across levels downward to biological neuroscience and upward to social factors, thereby elucidating the important cross-level interactions. Here the philosophy of biology literature on mechanisms can be a useful guide. Third, we have to trace the effects of these causal pathways back up into the mental realm, moving from the Jasperian level of explanation to that of understanding. This final effort will help us expand our empathic abilities to better understand how symptoms are experienced in the minds of our patients.
Response of the oligodendrocyte progenitor cell population (defined by NG2 labelling) to demyelination of the adult spinal cord (1998)

Elucidation of the response of oligodendrocyte progenitor cell populations to demyelination in the adult central nervous system (CNS) is critical to understanding why remyelination fails in multiple sclerosis. Using the anti-NG2 monoclonal antibody to identify oligodendrocyte progenitor cells, we have documented their response to antibody-induced demyelination in the dorsal column of the adult rat spinal cord. The number of NG2+ cells in the vicinity of demyelinated lesions increased by 72% over the course of 3 days following the onset of demyelination. This increase in NG2+ cell numbers did not reflect a nonspecific staining of reactive cells, as GFAP, OX-42, and Rip antibodies did not co-localise with NG2 + cells in double immunostained tissue sections. NG2 + cells incorporated BrdU 48-72 h following the onset of demyelination. After the onset of remyelination (10-14 days), the number of NG2+ cells decreased to 46% of control levels and remained consistently low for 2 months. When spinal cords were exposed to 40 Grays of x-irradiation prior to demyelination, the number of NG2+ cells decreased to 48% of control levels by 3 days following the onset of demyelination and remained unchanged at 3 weeks. Since 40 Grays of x-irradiation kills dividing cells, these studies illustrate a responsive and nonresponsive NG2+ cell population following demyelination in the adult spinal cord and suggest that the responsive NG2+ cell population does not renew itself.
Covalent modification and repressed transcription of a gene in hepatoma cells. (1981)

When liver cells undergo malignant transformation, certain genes cease being expressed. We have studied the structure of one such gene, whose protein product we have designated hepatic protein 22 (hp22), which is not expressed in the two Morris hepatomas studied. We have prepared a chimeric clone of pBR322 containing cDNA sequences complementary to mRNA coding for this protein. By using this cloned cDNA, we have examined changes in expression of this gene and changes in the restriction pattern of the DNA isolated from normal liver and these hepatomas. In both hepatomas, studies using the isoschizomeric pair of restriction enzymes Msp I and Hpa II have indicated hypermethylation of a cytosine residue within or proximal to the hp22 gene. Other differences in the restriction pattern between normal liver and hepatoma DNA were also detected with EcoRI and Ava I. Thus, in the nontranscribed form of this gene, the DNA has undergone covalent modification, distinguishing these two hepatomas from each other and from normal liver.
Eosinophilic oesophagitis in patients presenting with dysphagia – a prospective analysis (2008)

Eosinophilic oesophagitis was diagnosed in 12% of the patients presenting with dysphagia with relative risk of 9.5 if age <50 years. Oesophageal biopsies are warranted in patients presenting with dysphagia especially in the younger population. Patients may not present with classic endoscopic findings and EoO can be missed without biopsies.
MicroRNA Biomarkers in Whole Blood for Detection of Pancreatic Cancer (2014)

This study identified 2 diagnostic panels based on microRNA expression in whole blood with the potential to distinguish patients with pancreatic cancer from healthy controls. Further research is necessary to understand whether these have clinical implications for early detection of pancreatic cancer and how much this information adds to serum CA19-9.
Personal access to sequence databases on personal computers (1986)

A comprehensive package of software has been developed to access nucleic acid and protein sequence databases on stand-alone IBM personal computers. The software combines keyword search on the annotation fields of the data with pattern matching algorithms on the biological sequences. Sequences containing complex sites like promoters or kink sites can be identified as well as sequences that are similar to a query sequence. Protein sequences with particular patterns of amino acids such as hydrophobic regions can be identified as well. Considering the relatively inexpensive hard disks now available, personal computers have become a cost-effective alternative to mainframe processing for sequence databases.
Targeting the PI3K signaling pathway in cancer therapy (2012)

Small-molecule inhibitors targeting the PI3K/Akt/mTOR pathway show some success with these agents in current clinical trials. For further improvement in response, molecular correlates that can be used for patient selection, need to be determined. A more efficient and effective way to screen for patients to determine which patients are most likely to benefit from PI3K pathway inhibitors is also needed.
An Injectable 64 nW ECG Mixed-Signal SoC in 65 nm for Arrhythmia Monitoring (2014)

A syringe-implantable electrocardiography (ECG) monitoring system is proposed. The noise optimization and circuit techniques in the analog front-end (AFE) enable 31 nA current consumption while a minimum energy computation approach in the digital back-end reduces digital energy consumption by 40%. The proposed SoC is fabricated in 65 nm CMOS and consumes 64 nW while successfully detecting atrial fibrillation arrhythmia and storing the irregular waveform in memory in experiments using an ECG simulator, a live sheep, and an isolated sheep heart.
Automatic global vessel segmentation and catheter removal using local geometry information and vector field integration (2010)

Vessel enhancement and segmentation aim at (binary) per-pixel segmentation considering certain local features as probabilistic vessel indicators. We propose a new methodology to combine any local probability map with local directional vessel information. The resulting global vessel segmentation is represented as a set of discrete streamlines populating the vascular structures and providing additional connectivity and geometric shape information. The streamlines are computed by numerical integration of the directional vector field that is obtained from the eigenanalysis of the local Hessian indicating the local vessel direction. The streamline representation allows for sophisticated post-processing techniques using the additional information to refine the segmentation result with respect to the requirements of the particular application such as image registration. We propose different post-processing techniques for hierarchical segmentation, centerline extraction, and catheter removal to be used for X-ray angiograms. We further demonstrate how the global approach is able to significantly improve the segmentation compared to conventional local Hessian-based approaches.
Physiology and enzymology of thermophilic anaerobic bacteria degrading starch (1990)

The capability of secreting thermoactive enzymes exhibiting α-amylase and pullulanase with debraching activity, seems to be widely distributed amongst anaerobic thermophilic bacteria. Interestingly, pullulanase formed by these bacteria displays dual specificity by attacking α-1,6- as well as α-1,4-glycosidic linkages in branched glucose polymers. Unlike the enzyme system of aerobic microorganisms the majority of starch hydrolysing enzymes of anaerobic bacteria is metal indepedent and is extremely thermostable. This enzyme system is controlled by substrate induction and catabolite repression; enzyme expression is accomplished when maltose or maltose-containing carbohydrates are used as substrates. By developing a process in continuous culture we were able to greatly enhance enzyme synthesis and release by anaerobic thermophilic bacteria. An elevation in the specific activities of cell-free amylases and pullulanases could also be achieved by entrapping of bacteria in calcium alginate beads. The unique properties of extracellular enzymes of thermophilic anaerobic bacteria makes this group of organisms suitable candidates for inductrial application.
Blocking Soluble Tumor Necrosis Factor Signaling with Dominant-Negative Tumor Necrosis Factor Inhibitor Attenuates Loss of Dopaminergic Neurons in Models of Parkinson's Disease (2006)

The mechanisms that trigger or contribute to loss of dopaminergic (DA) neurons in Parkinson's disease (PD) remain unclear and controversial. Elevated levels of tumor necrosis factor (TNF) in CSF and postmortem brains of PD patients and animal models of PD implicate this proinflammatory cytokine in the pathophysiology of the disease; but a role for TNF in mediating loss of DA neurons in PD has not been clearly demonstrated. Here, we report that neutralization of soluble TNF (solTNF) in vivo with the engineered dominant-negative TNF compound XENP345 (a PEGylated version of the TNF variant A145R/I97T) reduced by 50% the retrograde nigral degeneration induced by a striatal injection of the oxidative neurotoxin 6-hydroxydopamine (6-OHDA). XENP345 was neuroprotective only when infused into the nigra, not the striatum. XENP345/6-OHDA rats displayed attenuated amphetamine-induced rotational behavior, indicating preservation of striatal dopamine levels. Similar protective effects were observed with chronic in vivo coinfusion of XENP345 with bacterial lipopolysaccharide (LPS) into the substantia nigra, confirming a role for solTNF-dependent neuroinflammation in nigral degeneration. In embryonic rat midbrain neuron/glia cell cultures exposed to LPS, even delayed administration of XENP345 prevented selective degeneration of DA neurons despite sustained microglia activation and secretion of solTNF. XENP345 also attenuated 6-OHDA-induced DA neuron toxicity in vitro. Collectively, our data demonstrate a role for TNF in vitro and in vivo in two models of PD, and raise the possibility that delaying the progressive degeneration of the nigrostriatal pathway in humans is therapeutically feasible with agents capable of blocking solTNF in early stages of PD.
Biology of Cachexia (1997)

About half of all cancer patients show a syndrome of cachexia, characterized by loss of adipose tissue and skeletal muscle mass. Such patients have a decreased survival time, compared with the survival time among patients without weight loss, and loss of total body protein leads to substantial impairment of respiratory muscle function. These changes cannot be fully explained by the accompanying anorexia, and nutritional supplementation alone is unable to reverse the wasting process. Despite a falling caloric intake, patients with cachexia frequently show an elevated resting energy expenditure as a result of increases in Cori cycle (i.e., catalytic conversion of lactic acid to glucose) activity, glucose and triglyceride-fatty acid cycling, and gluconeogenesis. A number of cytokines, including tumor necrosis factor-apha, interleukins 1 and 6, interferon gamma, and leukemia-inhibitory factor, have been proposed as mediators of the cachectic process. However, the results of a number of clinical and laboratory studies suggest that the action of the cytokines alone is unable to explain the complex mechanism of wasting in cancer cachexia. In addition, cachexia has been observed in some xenograft models even without a cytokine involvement, suggesting that other factors may be involved. These probably include catabolic factors, which act directly on skeletal muscle and adipose tissue and the presence of which has been associated with the clinical development of cachexia. A polyunsaturated fatty acid, eicosapentaenoic acid, attenuates the action of such catabolic factors and has been shown to stabilize the process of wasting and resting energy expenditure in patients with pancreatic cancer. Such a pharmacologic approach may provide new insights into the treatment of cachexia.
Antineoplastic Agents. 487. Synthesis and Biological Evaluation of the Antineoplastic Agent 3,4-Methylenedioxy-5,4‘-dimethoxy-3‘-amino-Z-stilbene and Derived Amino Acid Amides (2003)

An efficient synthesis of 3,4-methylenedioxy-5,4'-dimethoxy-3'-amino-Z-stilbene (1c) and hydrochloride (1d) is reported. The nitrostilbene intermediate 6a was obtained via a Wittig reaction using phosphonium salt 4 and 3-nitro-4-methoxybenzaldehyde 5. A one-step reduction using zinc in acetic acid produced the synthetic objective amine 1c. The coupling of this amine with various Fmoc amino acids, followed by cleavage of the alpha-amine protecting group, resulted in a series of new cancer cell growth inhibitory amides. Amine 1c, hydrochloride 1d, glycine amide 3b, and tyrosine amide 3f had the highest level (GI50 = 10(-2)-10(-3) micro g/mL) of activity against a panel of six human and one animal (P388) cancer cell lines. Amine 1c and its hydrochloride 1d potently inhibited tubulin polymerization by binding at the colchicine site, while the amides had little activity against purified tubulin. Nevertheless, most of the amides caused a marked increase in the mitotic index of treated cells, indicating that tubulin was their intracellular target.
Lack of H‐2 restriction of the Plasmodium falciparum (NANP) sequence as multiple antigen peptide (1991)

The major surface antigen of malaria sporozoites, the circumsporozoite protein, contains a region of tandem amino acid repeats, which in the case of the human malaria parasite Plasmodium falciparum, consist of four amino acids Asn-Ala-Asn-Pro (NANP) repeated up to about 40 times. This repetitive sequence has been considered as the basis for the development of subunit vaccines against P. falciparum malaria. We and others had previously shown that synthetic and recombinant NANP peptides were immunogenic only in H-2b mice. In the present report we show that, when mice with different H-2 haplotypes are immunized with the repetitive NANP sequence incorporated in a synthetic branching multiple antigen peptide (MAP), all except one of the mouse strains tested mounted an anti-peptide antibody response. Such a response does not appear to be due to the peculiar assembly of the NANP sequence. In fact, MAP containing repetitive sequences from circumsporozoite proteins of other malaria parasites did not overcome the genetic restriction of the immune response to the linear peptides. These data show that in the case of the P. falciparum NANP repeats, their immunogenicity can be dramatically changed and increased when these peptides are assembled as MAP. This unexpected finding may be of interest in the design of synthetic candidate malaria vaccines.
Magnesium-catalysed hydroboration of aldehydes and ketones (2012)

The heteroleptic magnesium alkyl complex [CH{C(Me)NAr}(2)Mg(n)Bu] (Ar = 2,6-(i)Pr(2)C(6)H(3)) is reported as a highly efficient pre-catalyst for the hydroboration of aldehydes and ketones with pinacolborane.
XXI.—The chlorination of iodophenols. Part III. The chlorination of o-iodophenol (1931)

S. Buchan and H. McCombie, J. Chem. Soc., 1931, 137 DOI: 10.1039/JR9310000137
A Fast Approximate Nearest Neighbor Search Algorithm in the Hamming Space (2012)

A fast approximate nearest neighbor search algorithm for the (binary) Hamming space is proposed. The proposed Error Weighted Hashing (EWH) algorithm is up to 20 times faster than the popular locality sensitive hashing (LSH) algorithm and works well even for large nearest neighbor distances where LSH fails. EWH significantly reduces the number of candidate nearest neighbors by weighing them based on the difference between their hash vectors. EWH can be used for multimedia retrieval and copy detection systems that are based on binary fingerprinting. On a fingerprint database with more than 1,000 videos, for a specific detection accuracy, we demonstrate that EWH is more than 10 times faster than LSH. For the same retrieval time, we show that EWH has a significantly better detection accuracy with a 15 times lower error rate.
Phycobilisome Ultrastructure and Chromatic Adaptation in Fremyella diplosiphon (1981)

Phycobilisomes isolated from the cyanobacterium Fremyella diplosiphon were negatively stained with uranyl sulphate and examined by transmission and scanning transmission electron microscopy. They were composed of a central triangular core of discs and six peripheral stacks of discs radiating out from the core. The peripheral stack discs were identified as phycobiliprotein hexamers on the basis of their size and morphology. Phycobilisomes from cells grown under white light were compared with phycobilisomes from cells grown under red light. The two types of phycobilisomes differed widely in their phycobiliprotein composition, but were closely similar in structure, varying only in the number of peripheral stack discs. The structure described here for F. diplosiphon phycobilisomes is consistent with a recently proposed model for cyanobacterial phycobilisomes.
In vivo targeted delivery of CD40 shRNA to mouse intestinal dendritic cells by oral administration of recombinant Sacchromyces cerevisiae (2014)

Short hairpin RNA (shRNA)-mediated gene regulation is a commonly used technique for gene manipulation. An efficient and safe delivery system is indispensable when shRNA is delivered into living organisms for gene therapy. Previous studies have proved that DNA and protein can be delivered into dendritic cells (DCs) by non-pathogenic Saccharomyces cerevisiae without being degraded. CD40 is closely related to apoptosis of tumor cells and some immune mechanisms. In this study, we demonstrated that recombinant yeast S. cerevisiae efficiently delivered the shRNA of immune-associated gene (CD40) into mouse intestinal DCs via oral administration. Western blot analysis of isolated intestinal DCs indicated that the inhibition of CD40 gene expression reached up to 56-91%. The secretion of cytokines such as interleukin-2 (IL-2), IL-6, IL-10, IL-12, tumor necrosis factor-α and interferon-γ in intestinal DCs had varying degrees of changes. In conclusion, we found that orally administered recombinant yeast can be used as an efficient shRNA delivery system for intestinal DC-specific gene silencing and immunomodulation in vivo.