Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of Topology on Hydraulic Conductivity in a Sand‐and‐Gravel Aquifer

A field experiment consisting of geophysical logging and tracer testing was conducted in a single well that penetrated a sand‐and‐gravel aquifer at the U.S. Geological Survey Toxic Substances Hydrology research site on Cape Cod, Massachusetts. Geophysical logs and flowmeter/pumping measurements were obtained to estimate vertical profiles of porosity ϕ, hydraulic conductivity K, temperature, and bulk electrical conductivity under background, freshwater conditions. Saline‐tracer fluid was then injected into the well for 2 h and its radial migration into the surrounding deposits was monitored by recording an electromagnetic‐induction log every 10 min. The field data are analyzed and interpreted primarily through the use of Archie's (1942) law to investigate the role of topological factors such as pore geometry and connectivity, and grain size and packing configuration in regulating fluid flow through these coarse‐grained materials. The logs reveal no significant correlation between K and ϕ, and imply that groundwater models that link these two properties may not be useful at this site. Rather, it is the distribution and connectivity of the fluid phase as defined by formation factor F, cementation index m, and tortuosity α that primarily control the hydraulic conductivity. Results show that F correlates well with K, thereby indicating that induction logs provide qualitative information on the distribution of hydraulic conductivity. A comparison of α, which incorporates porosity data, with K produces only a slightly better correlation and further emphasizes the weak influence of the bulk value of ϕ on K.
A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks*S

Protein-protein interaction mapping has progressed rapidly in recent years, enabling the completion of several high throughput studies. However, knowledge of physical interactions is limited for numerous classes of proteins, such as chromatin-bound proteins, because of their poor solubility when bound to DNA. To address this problem, we have developed a novel method, termed modified chromatin immunopurification (mChIP), that allows for the efficient purification of protein-DNA macromolecules, enabling subsequent protein identification by mass spectrometry. mChIP consists of a single affinity purification step whereby chromatin-bound protein networks are isolated from mildly sonicated and gently clarified cellular extracts using magnetic beads coated with antibodies. We applied the mChIP method in Saccharomyces cerevisiae cells expressing endogenously tandem affinity purification (TAP)-tagged histone H2A or the histone variant Htz1p and successfully co-purified numerous chromatin-bound protein networks as well as DNA. We further challenged the mChIP procedure by purifying three chromatin-bound bait proteins that have proven difficult to purify by traditional methods: Lge1p, Mcm5p, and Yta7p. The protein interaction networks of these three baits dramatically expanded our knowledge of their chromatin environments and illustrate that the innovative mChIP procedure enables an improved characterization of chromatin-associated proteins.
[Correlation of histological classifications of gastric carcinomas with location and prognosis].

AIM To evaluate the prognostic impact of different histological classifications of gastric adenocarcinoma. METHODS Between 1993-2000, 94 patients with gastric adenocarcinoma were studied. Tumors were classified according to TNM staging, WHO, Lauren and Goseki classifications. Twenty five patients (27%) had a proximal tumor and 69 (73%) a distal tumor. Intestinal type according to Lauren were more often observed among the proximal carcinomas (19/25) than in distal ones (32/69) (P=0.01). According to Goseki, lymph node metastasis were less frequently found in group III (5/13) than in other groups (64/81) (P=0.033). The mean follow-up was 23 months. Survical was not influenced by WHO, Lauren, and Goseki classifications. Survival significantly varied according to the different groups of the TNM classification. The proximal location of the tumor was associated with poorer prognosis than distal location (P=0.0373). Number of metastatic lymph nodes, invasion of perineurium, and vascular invasion had significant prognostic value in proximal carcinomas. CONCLUSION The results of this study suggest that gastric carcinomas should be divided into proximal and distal tumors using the Goseki classification in addition to the Lauren classification because the Goseki classification recognizes tumor groups with different dissemination routes.
Selective Logging, Habitat Quality and Home Range Use by Sympatric Gorillas and Chimpanzees: A Case Study from an Active Logging Concession in Southeast Cameroon

We examined range use by great apes during logging activities and investigated associations between local variations in ape abundance and changes in the structure of the habitat or in the availability of fruits after disturbances. We carried out two annual censuses of western lowland gorilla (G. g. gorilla) and chimpanzee populations (Pan t. troglodytes) in an active logging concession in Southeast Cameroon. The results suggest that gorillas may adapt their range use to avoid most recently logged compartments, while chimpanzees appear to be more spatially resilient to logging. In our study site, selective logging affected 10% of the forest. After logging, gorillas nested in all types of vegetation, while chimpanzees nested exclusively in mixed mature forest. Fruit availability was not affected by logging and did not explain the distribution of ape nests in the study area.
A mouse model of inflammatory root resorption induced by pulpal infection.

OBJECTIVE The present study was undertaken to determine the frequency and extent of apical root resorption associated with induced periradicular lesions in mice. STUDY DESIGN Bone and root resorption was quantified by using two- and three-dimensional micro-computed tomography (mu-CT) in the lower first molars of mice subjected to pulp exposure and infection. RESULTS mu-CT measurements showed significant apical resorption in exposed and infected teeth, resulting in an average distal root shortening of 12.7% (P <.001 vs unexposed). These findings were confirmed with three-dimensional reconstituted images that showed thinning and shortening of the distal root. Tartrate-resistant acid phosphatase clastic cells were associated with resorption lacunae on the cementum of root apices, as well as on bone at the periphery of the periradicular lesions. Brown and Brenn staining showed the presence of bacteria in dentinal tubules adjacent to resorbed cementum. CONCLUSIONS Apical root resorption is a prominent and consistent finding associated with periradicular infection in the mouse. This species represents a convenient model for studying the pathogenesis of inflammatory root resorption in vivo.
Development of a physiologic-based pharmacokinetic model for estimating sulfamethazine concentrations in swine and application to prediction of violative residues in edible tissues.

OBJECTIVE To develop a flow-limited, physiologic-based pharmacokinetic model for use in estimating concentrations of sulfamethazine after IV administration to swine. SAMPLE POPULATION 4 published studies provided physiologic values for organ weights, blood flows, clearance, and tissue-to-blood partition coefficients, and 3 published studies provided data on plasma and other tissue compartments for model validation. PROCEDURE For the parent compound, the model included compartments for blood, adipose, muscle, liver, and kidney tissue with an extra compartment representing the remaining carcass. Compartments for the N-acetyl metabolite included the liver and the remaining body. The model was created and optimized by use of computer software. Sensitivity analysis was completed to evaluate the importance of each constant on the whole model. The model was validated and used to estimate a withhold interval after an IV injection at a dose of 50 mg/kg. The withhold interval was compared to the interval estimated by the Food Animal Residue Avoidance Databank (FARAD). RESULTS Specific tissue correlations for plasma, adipose, muscle, kidney, and liver tissue compartments were 0.93, 0.86, 0.99, 0.94, and 0.98, respectively. The model typically overpredicted concentrations at early time points but had excellent accuracy at later time points. The withhold interval estimated by use of the model was 120 hours, compared with 100 hours estimated by FARAD. CONCLUSIONS AND CLINICAL RELEVANCE Use of this model enabled accurate prediction of sulfamethazine pharmacokinetics in swine and has applications for food safety and prediction of drug residues in edible tissues.
The Nipple‐Areolar Complex

Objective. The purpose of this presentation is to show the radiologic findings of normal variants and benign and malignant diseases that affect the nipple‐areolar complex. Methods. We evaluated the imaging findings of nipple‐areolar complex lesions, using multiple breast imaging modalities including mammography, sonography, galactography, contrast‐enhanced magnetic resonance imaging (MRI), and positron emission tomography/computed tomography. Results. Radiologic features of nipple‐areolar complex lesions, including Montgomery tubercles, nipple inversion, benign calcifications, inflammation, duct dilatations, intraductal papillomas, fibroadenomas, neurofibromatosis, dermatosis of the nipple, and breast malignancy, have been illustrated. Conclusions. A clinical examination is essential and an appropriate imaging evaluation with multiple modalities is often necessary to accurately diagnose an underlying abnormality of the nipple‐areolar complex. Given the limitations of conventional mammography, supplemental mammographic views often are needed, and sonography may be performed to further characterize a mammographic or clinical finding. Also, contrast‐enhanced MRI may be useful for additional evaluation.
Effects of the Two Somatostatin Variants Somatostatin‐14 and [Pro2, Met13]Somatostatin‐14 on Receptor Binding, Adenylyl Cyclase Activity and Growth Hormone Release from the Frog Pituitary

Two isoforms of somatostatin from frog brain have been recently characterized, namely somatostatin‐14 (SS1) and [Pro2, Met13]somatostatin‐14 (SS2). The genes encoding for the precursors of these two somatostatin variants are expressed in hypothalamic nuclei involved in the control of the frog pituitary. The aim of the present study was to investigate the effect of SS1 and SS2 on adenohypophysial cells. Autoradiographic studies using [125I‐Tyr°, d‐Trp8] SS1 as a radioligand revealed that somatostatin binding sites are evenly distributed in the frog pars distalis. The SS2 variant was significantly (P<0.01) more potent than SS1 in competing with the radioligand (IC50=1.2±0.2 and 5.6±0.6 nM, respectively). Both SS1 and SS2 induced a modest but significant reduction in cAMP formation in dispersed distal lobe cells but did not affect spontaneous growth hormone (GH) release. Synthetic human GRF (hGRF) induced a significant increase in cAMP accumulation and GH release in this system. Both SS1 and SS2 inhibited the stimulatory effects of hGRF on cAMP formation and GH secretion. These data show that the SS1 and SS2 variants can regulate adenohypophysial functions. The fact that GH cells are exclusively located in the dorsal area of the frog adenohypophysis, while somatostatin receptors are present throughout the pars distalis, indicates that the two somatostatin isoforms may control the secretion of pituitary hormones additional to GH in amphibians.
Hepatocellular Carcinoma in a Tertiary Referral Hospital in Indonesia: Lack of Improvement of One-Year Survival Rates between 1998-1999 and 2013-2014.

BACKGROUND The survival of hepatocellular carcinoma (HCC) patients is usually low due to late diagnosis. Cipto Mangunkusumo Hospital as the largest tertiary referral hospital in Indonesia, has recently improved its modalities for advanced HCC management, but there has not been any evaluation on any improvement in HCC patient survival. MATERIALS AND METHODS A retrospective analysis on 114 HCC patients in 2013-2014 were conducted and compared with the database for 77 HCC patients in 1998-1999. Clinical characteristics and treatment received were recorded and the survival of both groups was analyzed using the Kaplan-Meier method and compared using the log-rank test. RESULTS The percentage of HBV positive patients had increased after fifteen years from 32.5% to 67.5%. Only two patients (1.8%) in 2013-2014 were diagnosed with HCC during surveillance program. Proportions of Barcelona Clinic Liver Cancer A, B, C, and D in 2013-2014 were 1.8%, 42%, 28.1%, and 28.1%, respectively. There was an increase in the use of potentially curative treatment, such as surgical resection or combination of loco-regional therapies. The one-year survival rate increased from 24.1% in 1998-1999 to 29.4% in 2013-2014, while the median survival decreased from 146 days to 138 days, but the difference was not statistically significant (p=0.913). CONCLUSIONS There was no improvement in the median survival of HCC patients after fifteen years because most continued to present at late stages. There is an urgent need for a nationwide implementation of a hepatitis screening program and HCC surveillance education.
Hypoxic regulation of mRNA expression

Many tumors are hypoxic, and cells that are experimentally rendered hypoxic display a variety of phenotypes which allow them to adapt to the micro-environment. These phenotypes include a shift from aerobic to anaerobic metabolism, a diminution of reactive oxygen species, an arrest of proliferation, apoptosis, and a secretion of pro-angiogenic growth factors. Some of these hypoxic phenotypes are re-capitulated in normoxic tumor cells (e.g. an increase in anaerobic metabolism), and some tumors have undergone mutations that allow them to bypass the cell cycle arrest and apoptosis typically seen in hypoxic cells. Hypoxic regulation of gene expression is responsible for many hypoxia-induced phenotypes, and here we review a variety of mechanisms by which gene expression is altered in hypoxic cells. These include transcription by HIF-1, the hypoxia inducible transcription factor, and other hypoxia-inducible transcription factors, including ones generated by hypoxic activation of the integrated stress response. Recent data from our laboratory demonstrate that nonsense mediated RNA decay is also regulated in hypoxic cells and thus may play an important role in hypoxic gene regulation and hypoxic phenotypes.
Clinical Versus Administrative Data Bases for CABG Surgery: Does it Matter

This study compared the ability of a clinical and administrative data base in New York State to predict in-hospital mortality and to assess hospital performance for coronary artery bypass graft surgery. The results indicated that the clinical data base, the Cardiac Surgery Reporting System, is substantially better at predicting case-specific mortality than the administrative data base, the Statewide Planning and Research Cooperative System. Also, correlations between hospital mortality rates that are risk-adjusted using the two systems were only moderately high (0.75 to 0.80). The addition of new risk factors from the Statewide Planning and Research Cooperative System improved the predictive power of both systems but did not diminish the difference in effectiveness of the two systems. The three unique clinical risk factors in the Cardiac Surgery Reporting System (ejection fraction, reoperation, and more than 90% narrowing of the left main trunk) seemed to account for much of the difference in effectiveness of the two systems.
Six1 and Eya1 Expression Can Reprogram Adult Muscle from the Slow-Twitch Phenotype into the Fast-Twitch Phenotype

ABSTRACT Muscle fibers show great differences in their contractile and metabolic properties. This diversity enables skeletal muscles to fulfill and adapt to different tasks. In this report, we show that the Six/Eya pathway is implicated in the establishment and maintenance of the fast-twitch skeletal muscle phenotype. We demonstrate that the MEF3/Six DNA binding element present in the aldolase A pM promoter mediates the high level of activation of this promoter in fast-twitch glycolytic (but not in slow-twitch) muscle fibers. We also show that among the Six and Eya gene products expressed in mouse skeletal muscle, Six1 and Eya1 proteins accumulate preferentially in the nuclei of fast-twitch muscles. The forced expression of Six1 and Eya1 together in the slow-twitch soleus muscle induced a fiber-type transition characterized by the replacement of myosin heavy chain I and IIA isoforms by the faster IIB and/or IIX isoforms, the activation of fast-twitch fiber-specific genes, and a switch toward glycolytic metabolism. Collectively, these data identify Six1 and Eya1 as the first transcriptional complex that is able to reprogram adult slow-twitch oxidative fibers toward a fast-twitch glycolytic phenotype.
Prevalence of persistent vegetative state in patients with severe traumatic brain injury and its trend during the past four decades: A meta-analysis.

BACKGROUND Estimating the prevalence of persistent vegetative state (PVS) following severe traumatic brain injury (sTBI) and its change over time is important for the study of the disease. OBJECTIVE To estimate the prevalence of PVS at six months after sTBI and its trend over the past four decades, and to explore the effect of demographic data, such as age and sex, on the prevalence of PVS. METHOD Observational studies presenting the prevalence of PVS or the number of patients with PVS at six months after sTBI were included in the analysis. The overall prevalence and prevalence within pre-defined time intervals were calculated and meta-regression analysis was performed to assess the effect of age, gender, and time on the prevalence. RESULTS Twenty articles reporting 21 cohort studies were included. The overall prevalence of PVS at six months after injury was 2.77% (95% CI 0.0204-0.0375). There was no statistically significant trend towards time (P = 0.77). And we found no differences in prevalence according to age (P = 0.68) and gender (P = 0.57). CONCLUSIONS Prevalence of PVS at six months after sTBI has no significant change over the past four decades. Age and gender do not seem to have a significant effect on the prevalence.
QoS Mesh Routing Protocol for IEEE 802.16 based Wireless Mesh Networks

This paper proposes QoS Mesh routing protocol for IEEE 802.16 based wireless mesh networks. QoS Mesh Routing Protocol proposed in this paper is a proactive hop-by-hop QoS routing protocol. The goal of our protocol is not only to find routes from a source to a destination node, but also optimal routes that satisfies QoS requirements, given in terms of bandwidth and delay as default QoS parameters. In this paper, we first analyze possible types of routing protocols that have been studied for MANET and show proactive hop-by-hop routing protocols are the most appropriate for wireless mesh networks. Then, we present a network model for IEEE 802.16 based wireless mesh networks and propose a proactive hop-by-hop QoS routing protocol. Through our simulation, we represent that our routing protocol outperforms QOLSR protocol in terms of end-to-end delay, packet delivery ratio and routing overhead.
Targeted Inactivation of Mapk4 in Mice Reveals Specific Nonredundant Functions of Erk3/Erk4 Subfamily Mitogen-Activated Protein Kinases

ABSTRACT Erk4 and Erk3 are atypical members of the mitogen-activated protein (MAP) kinase family. The high sequence identity of Erk4 and Erk3 proteins and the similar organization of their genes imply that the two protein kinases are paralogs. Recently, we have shown that Erk3 function is essential for neonatal survival and critical for the establishment of fetal growth potential and pulmonary function. To investigate the specific functions of Erk4, we have generated mice with a targeted disruption of the Mapk4 gene. We show that Erk4-deficient mice are viable and fertile and exhibit no gross morphological or physiological anomalies. Loss of Erk4 is not compensated by changes in Erk3 expression or activity during embryogenesis or in adult tissues. We further demonstrate that additional loss of Erk4 does not exacerbate the fetal growth restriction and pulmonary immaturity phenotypes of Erk3−/− mice and does not compromise the viability of Erk3+/− neonates. Interestingly, behavioral phenotyping revealed that Erk4-deficient mice manifest depression-like behavior in the forced-swimming test. Our analysis indicates that the MAP kinase Erk4 is dispensable for mouse embryonic development and reveals that Erk3 and Erk4 have acquired specialized functions through evolutionary diversification.
Contributions of culture and antimicrobial susceptibility tests to the retreatment of patients with pulmonary tuberculosis.

INTRODUCTION This study evaluated the efficacy of retreatment of pulmonary tuberculosis (TB) with regard to treatment outcomes and antimicrobial susceptibility testing (ST) profiles. METHODS This retrospective cohort study analyzed 144 patients treated at a referral hospital in Brazil. All of them had undergone prior treatment, were smear-positive for TB and received a standardized retreatment regimen. Fisher’s 2-tailed exact test and the χ² test were used; RRs and 95% CIs were calculated using univariate and multivariate binary logistic regression. RESULTS The patients were cured in 84 (58.3%) cases. Failure was associated with relapsed treatment and abandonment (n=34). Culture tests were obtained for 103 (71.5%) cases; 70 (48.6%) had positive results. ST results were available for 67 (46.5%) cases; the prevalence of acquired resistance was 53.7%. There were no significant differences between those who achieved or not therapeutic success (p=0.988), despite being sensitive or resistant to 1 or more drugs. Rifampicin resistance was independently associated with therapeutic failure (OR: 4.4, 95% CI:1.12-17.37, p=0.034). For those cases in which cultures were unavailable, a 2nd model without this information was built. In this, return after abandonment was significantly associated with retreatment failure (OR: 3.59, 95% CI:1.17-11.06, p=0.026). CONCLUSIONS In this cohort, the general resistance profile appeared to have no influence on treatment outcome, except in cases of rifampicin resistance. The form of reentry was another independent predictor of failure. The use of bacterial culture identification and ST in TB management must be re-evaluated. The recommendations for different susceptibility profiles must also be improved.