Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface Photometric Calibration of the Infrared Tully-Fisher Relation Using Cepheid-based Distances of Galaxies

Infrared J and H surface photometry are carried out for nearby 12 galaxies whose distances have been accurately measured via Hubble Space Telescope Cepheid observations. Using the total, isophotal, and surface photometric aperture magnitudes, we calibrate the infrared luminosity-line-width relation (IRTF). It is found that IRTF changes its slope at log W ~ 2.45 in all the examined magnitude systems. The apparent scatter of IRTF is not significantly reduced when surface photometric magnitudes are used instead of the conventionally used synthetic aperture magnitude H-0.5. It is also shown that the color (I-H)T of the nearby calibrator galaxies is redder by ~0.2 mag than the Coma Cluster of galaxies, but such a trend is not clearly visible for Ursa Major mostly because of poor statistics. The color offset of the Coma Cluster is analogous to that previously found in IT - H-0.5. From the present calibration of H-band IRTF, we obtain the distance to the Coma Cluster to be m - M = 34.94 ± 0.13 mag, where no account is taken of the I-H color problem. Using the cosmic microwave background rest recession velocity of the Coma Cluster, we obtain H0 = 73 ± 4 km s-1 Mpc-1.
In-kind and out-of-kind penalties: Preference and valuation

Utilitarian and economic theories of deterrence hold that the relation of the penalty to the misdeed should be irrelevant. In five experiments using hypothetical cases, judgments of penalties depended on whether this relation was in-kind (IK) or out-of-kind (OK). When victims were identifiable, IK penalties were higher than OK and preferred to OK. Subjects seemed to confuse penalties and compensation. When there were no identifiable victims (e.g., environmental damage), IK penalties were preferred, but OK penalties were higher. Here, OK judgments were more uncertain, and subjects preferred to err on the side of overpunishing. The results can be explained in terms of overgeneralization of usuallyuseful heuristics. Alternative hypotheses concerning aggression and scale compatibility are rejected. The findings have implications for the setting of penalties in legal cases (e.g., the Exxon Valdez) and for lay theories of punishment in non-legal settings.
Late Weichselian pollen stratigraphy, clay varve chronology and palaeomagnetic secular variations in Lake Bolmen, Småland, south Sweden

Pollen analysis, glacial varve chronology and palaeomagnetic measurements were carried out on Late Weichselian lake sediments from southwestern Smaland, south Sweden. The sequence is correlated to the GRIP event stratigraphy, expressed in calendar years BP, and covers the period from the deglaciation at c. 14 400 to 11 300 calendar years BP. The series encompasses c. 930 varves and has been connected to the local varve chronology. Varve thickness increases markedly after the Older Dryas stadial, which indicates an accelerated deglaciation and melting of dead ice. The pollen diagram displays the vegetation development from the deglaciation at c. 14 400 calendar years BP to the transition to the Holocene. The vegetation succession starts with an arctic pioneer vegetation at the deglaciation, changes to a more stable tundra environment and displays a development which concurs with the traditional lateglacial pollen stratigraphy for southern Sweden. A palaeo‐magnetic secular variation curve is presented displaying two westerly declination swings at 14200‐13800 and 12 800‐11 600 calendar years BP, respectively. The upper one can be recognized from other palaeomagnetic stratigraphies from southern Sweden and Estonia.
The Inverse Gaussian Process as a Degradation Model

This article systematically investigates the inverse Gaussian (IG) process as an effective degradation model. The IG process is shown to be a limiting compound Poisson process, which gives it a meaningful physical interpretation for modeling degradation of products deteriorating in random environments. Treated as the first passage process of a Wiener process, the IG process is flexible in incorporating random effects and explanatory variables that account for heterogeneities commonly observed in degradation problems. This flexibility makes the class of IG process models much more attractive compared with the Gamma process, which has been thoroughly investigated in the literature of degradation modeling. The article also discusses statistical inference for three random effects models and model selection. It concludes with a real world example to demonstrate the applicability of the IG process in degradation analysis. Supplementary materials for this article are available online.
Sources of increase in lowermost stratospheric sulphurous and carbonaceous aerosol background concentrations during 1999–2008 derived from CARIBIC flights

This study focuses on sulphurous and carbonaceous aerosol, the major constituents of particulate matter in the lowermost stratosphere (LMS), based on in situ measurements from 1999 to 2008. Aerosol particles in the size range of 0.08–2 µm were collected monthly during intercontinental flights with the CARIBIC passenger aircraft, presenting the first long-term study on carbonaceous aerosol in the LMS. Elemental concentrations were derived via subsequent laboratory-based ion beam analysis. The stoichiometry indicates that the sulphurous fraction is sulphate, while an O/C ratio of 0.2 indicates that the carbonaceous aerosol is organic. The concentration of the carbonaceous component corresponded on average to approximately 25% of that of the sulphurous, and could not be explained by forest fires or biomass burning, since the average mass ratio of Fe to K was 16 times higher than typical ratios in effluents from biomass burning. The data reveal increasing concentrations of particulate sulphur and carbon with a doubling of particulate sulphur from 1999 to 2008 in the northern hemisphere LMS. Periods of elevated concentrations of particulate sulphur in the LMS are linked to downward transport of aerosol from higher altitudes, using ozone as a tracer for stratospheric air. Tropical volcanic eruptions penetrating the tropical tropopause are identified as the likely cause of the particulate sulphur and carbon increase in the LMS, where entrainment of lower tropospheric air into volcanic jets and plumes could be the cause of the carbon increase.
Centromere Protein B Null Mice are Mitotically and Meiotically Normal but Have Lower Body and Testis Weights

CENP-B is a constitutive centromere DNA-binding protein that is conserved in a number of mammalian species and in yeast. Despite this conservation, earlier cytological and indirect experimental studies have provided conflicting evidence concerning the role of this protein in mitosis. The requirement of this protein in meiosis has also not previously been described. To resolve these uncertainties, we used targeted disruption of the Cenpb gene in mouse to study the functional significance of this protein in mitosis and meiosis. Male and female Cenpb null mice have normal body weights at birth and at weaning, but these subsequently lag behind those of the heterozygous and wild-type animals. The weight and sperm content of the testes of Cenpb null mice are also significantly decreased. Otherwise, the animals appear developmentally and reproductively normal. Cytogenetic fluorescence-activated cell sorting and histological analyses of somatic and germline tissues revealed no abnormality. These results indicate that Cenpb is not essential for mitosis or meiosis, although the observed weight reduction raises the possibility that Cenpb deficiency may subtly affect some aspects of centromere assembly and function, and result in reduced rate of cell cycle progression, efficiency of microtubule capture, and/or chromosome movement. A model for a functional redundancy of this protein is presented.
Temporal variations in Holocene slip rate along the central Garlock fault, Pilot Knob Valley, California

Average geologic slip rates along the central Garlock fault, in eastern California, are thought to have been relatively steady at 5–7 mm/yr since at least the Late Pleistocene, yet present-day rates inferred from geodetic velocity fields are indistinguishable from zero. We evaluate the possibility of non-steady slip over millennial timescales using displaced Late Holocene alluvium along the central Garlock fault in Pilot Knob Valley. Truncation of a Late Holocene alluvial fan deposit against a shutter ridge requires a minimum of 30–37 m of displacement since deposition of the fan; maximum allowable displacement is 43–50 m. The extent of soil development atop the fan surface and optically stimulated luminescence ages bracket fan deposition between 3.5 and 4.5 ka. Together, these data require that slip rates during the Late Holocene were ∼7–14 mm/yr, with a preferred rate of ∼11–13 mm/yr. Our results, in conjunction with previous estimates of displacement over the past ∼15 ka, require significant temporal variations in strain release along the Garlock fault and confirm previous suggestions that interactions among fault systems in eastern California give rise to alternating periods of fault activity and quiescence.
Extrinsic Modulation and Motor Pattern Generation in a Feeding Network: a Cellular Study

Systems level studies have shown that the paired serotonergic cerebral giant cells (CGCs) of gastropod mollusks have important extrinsic modulatory actions on the central pattern generator (CPG) underlying rhythmic ingestion movements. Here we present the first study that investigates the modulatory actions of the CGCs and their released transmitter 5-HT on the CPG at the cellular level. In the snail, Lymnaea, motoneurons such as the B4, B8, and B4CL cells are part of the feeding CPG and receive serotonergic synaptic inputs from CGCs. These motoneurons were used to investigate the effect of serotonergic modulation on endogenous cellular properties of CPG neurons. Cells were isolated from the intact nervous system, and their properties were examined by pharmacological methods in cell culture. Motoneurons were also grown in coculture with CGCs to compare 5-HT effects with CGC stimulation. Three distinct modulatory effects of exogenously applied 5-HT/CGC activity were seen: all three motoneuron types were depolarized by 5-HT for prolonged periods leading to firing. Conditional bursting accompanied this depolarization in the B4/B8 cells, but not in B4CL cells. The frequency of the bursting was increased with increased CGC tonic firing. An increase in the size of postinhibitory rebound (PIR) occurred with 5-HT application in all three cell types, because of an increase in a CsCl-sensitive, hyperpolarization-activated inward current. Similar modulatory effects on membrane potential, endogenous bursting, and PIR properties could be observed in the intact nervous system and were necessary for motoneuron activation during feeding. Part of the systems gating and frequency control functions of the CGCs appear to be caused by these modulatory effects on feeding motoneurons.
Associations between BRCA Mutations in High-Risk Breast Cancer Patients and Familial Cancers Other than Breast or Ovary

Purpose We investigated the relationship between BRCA mutations and the distribution of familial cancers other than breast or ovary in high-risk breast cancer patients. Methods Patients with breast cancer who had at least one of the following risk factors were enrolled: reported family history of breast or ovarian cancer; 40 years of age or younger age at diagnosis; bilateral breast cancer; or male gender. Genetic testing for BRCA mutation and questionnaires about personal and family histories of malignancies were performed. Results Among the 238 eligible patients, 49 (20.6%) patients had BRCA1/2 mutations, which were more frequent in patients with multiple risk factors (p<0.0001). There were 271 members of 156 (65.5%) families who had histories of other primary cancer. The distribution of the families was 119 (63.0%) and 37 (75.5%) in the BRCA-negative and positive group, respectively (p=0.0996). Multiple familial cancers occurred in 70 families, which were significantly more frequent in BRCA-positive families (p=0.0034). By ordinal logistic regression, the occurrence of multiple familial cancers was associated with BRCA mutations (p=0.0045), not with other risk factors. The most common site of disease was the stomach, which is the most common in nationwide. And the proportional incidence of pancreatic cancer (6.8%) was significantly higher than that of nationwide cancer statistics (2.4%, p=0.0137). Conclusion BRCA mutations in high-risk breast cancer patients were associated with multiple risk factors and multiple family members with other primary cancers. Genetic counseling based on accurate information should be provided to families with BRCA mutation carriers.
Regulation of Cell Proliferation by Fast Myosin Light Chain 1 in Myoblasts Derived from Extraocular Muscle, Diaphragm and Gastrocnemius

The extraocular muscle (EOM) suffers much less injury from Duchenne muscular dystrophy (DMD) than other skeletal muscles such as diaphragm and gastrocnemius. The present study was undertaken to test the hypothesis that differential expression of regulatory proteins between the EOM and other skeletal muscles is responsible for the observed difference in the sensitivity to DMD-associated damage. Protein expression in the tissue samples obtained from EOM, diaphragm or gastrocnemius of C57BL/6 mice was analyzed by two-dimensional gel electrophoresis and mass spectrometry. There were 35 proteins that were identified to be differentially expressed among different skeletal muscle tissues. Among the 35 proteins, a fast skeletal muscle isoform myosin light chain 1 (MLC1f) protein was further studied in relation to muscle cell proliferation. The EOM-derived myoblasts had much lower levels of MLC1f and higher rate of cell proliferation in contrast to the myoblasts derived from diaphragm or gastrocnemius, which displayed a higher expression of MLC1f along with a slow proliferation. Deletion of MLC1f using siRNA targeting MLC1f resulted in an increased rate of cell proliferation in the myoblasts. Cell cycle analysis revealed that MLC1f inhibited the transition of the cell cycle from the G1 to the S phase. Therefore, the present study demonstrates that MLC1f may negatively regulate proliferation of myoblasts through inhibition of the transition from the G1 to the S phase of the cell cycle. Low levels of MLC1f in myoblasts of EOM may ensure cell proliferation and enhance the repair process for EOM under the DMD disease condition, thus making EOM suffer less injury from DMD.
Prognostic implications of periodic epileptiform discharges.

BACKGROUND Periodic epileptiform discharges (PEDs) are an abnormal finding on electroencephalograms (EEGs), the significance of which is uncertain. OBJECTIVE To investigate long-term outcome in patients with PEDs. DESIGN We retrospectively analyzed the outcomes of patients who had PEDs diagnosed during a 7-year period. We abstracted and tabulated clinical parameters from the time of EEG, imaging findings, EEG measurements, and subsequent clinical outcome from medical records. We used descriptive, inferential, and logistic regression analysis to determine the factors associated with clinical outcomes in patients with PEDs. We divided PEDs into the following subgroups: periodic lateralized epileptiform discharges (PLEDs), generalized PEDs, and bilateral PEDs and analyzed these subgroups individually. SETTING University-affiliated teaching hospital. Subjects One hundred sixty-two patients with PEDs. RESULTS We obtained complete clinical, neuroimaging, neurophysiologic, and long-term outcome data in 118 patients. In the subgroup of patients with PLEDs, absence of seizures at onset (odds ratio, 0.21 per point; 95% confidence interval, 0.04-0.97) and an acute etiology for the PLEDs (odds ratio, 0.14 per point; 95% confidence interval, 0.03-0.72) were associated with death. A nonneoplastic cause for PLEDs was associated with independent functionality (odds ratio, 0.45 per point; 95% confidence interval, 0.3-0.67). CONCLUSION In patients with PLEDs, the absence of clinical seizures at the time of detection and presumed acute etiology are associated with death, whereas a nonneoplastic etiology was associated with a good clinical outcome.
Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms

Tania Quesada1,2*, Zhen Li3*, Christopher Dervinis2, Yao Li3, Philip N. Bocock1,2, Gerald A. Tuskan4,5, George Casella3,6, John. M. Davis1,2,6 and Matias Kirst1,2,6 1Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA; 2School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA; 3Department of Statistics, University of Florida, PO Box 118545, Gainesville, FL 32611-8545, USA; 4Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA; 5Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr, Knoxville, TN, 37996-4561, USA; 6University of Florida Genetics Institute,
Identification and Functional Characterization of a Tonoplast Dicarboxylate Transporter in Tomato (Solanum lycopersicum)

Acidity plays an important role in flavor and overall organoleptic quality of fruit and is mainly due to the presence of organic acids. Understanding the molecular basis of organic acid metabolism is thus of primary importance for fruit quality improvement. Here, we cloned a putative tonoplast dicarboxylate transporter gene (SlTDT) from tomato, and submitted it to the NCBI database (GenBank accession number: KC733165). SlTDT protein contained 13 putative transmembrane domains in silico analysis. Confocal microscopic study using green fluorescent fusion proteins revealed that SlTDT was localized on tonoplast. The expression patterns of SlTDT in tomato were analyzed by RT-qPCR. The results indicated that SlTDT expressed in leaves, roots, flowers and fruits at different ripening stages, suggesting SlTDT may be associated with the development of different tissues. To further explore the function of SlTDT, we constructed both overexpression and RNAi vectors and obtained transgenic tomato plants by agrobacterium-mediated method. Gas chromatography-mass spectrometer (GC-MS) analysis showed that overexpression of SlTDT significantly increased malate content, and reduced citrate content in tomato fruit. By contrast, repression of SlTDT in tomato reduced malate content of and increased citrate content. These results indicated that SlTDT played an important role in remobilization of malate and citrate in fruit vacuoles.
Molecular Dissection of a Yeast Septin: Distinct Domains Are Required for Septin Interaction, Localization, and Function

ABSTRACT The septins are a family of cytoskeletal proteins present in animal and fungal cells. They were first identified for their essential role in cytokinesis, but more recently, they have been found to play an important role in many cellular processes, including bud site selection, chitin deposition, cell compartmentalization, and exocytosis. Septin proteins self-associate into filamentous structures that, in yeast cells, form a cortical ring at the mother bud neck. Members of the septin family share common structural domains: a GTPase domain in the central region of the protein, a stretch of basic residues at the amino terminus, and a predicted coiled-coil domain at the carboxy terminus. We have studied the role of each domain in the Saccharomyces cerevisiae septin Cdc11 and found that the three domains are responsible for distinct and sometimes overlapping functions. All three domains are important for proper localization and function in cytokinesis and morphogenesis. The basic region was found to bind the phosphoinositides phosphatidylinositol 4-phosphate and phosphatidylinositol 5-phosphate. The coiled-coil domain is important for interaction with Cdc3 and Bem4. The GTPase domain is involved in Cdc11-septin interaction and targeting to the mother bud neck. Surprisingly, GTP binding appears to be dispensable for Cdc11 function, localization, and lipid binding. Thus, we find that septins are multifunctional proteins with specific domains involved in distinct molecular interactions required for assembly, localization, and function within the cell.
Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1.

BACKGROUND Definitive diagnosis of primary hyperoxaluria type 1 (PH1) requires analysis of alanine:glyoxylate aminotransferase (AGT) activity in the liver. We have previously shown that targeted screening for the 3 most common mutations in the AGXT gene (c.33_34insC, c.508G>A, and c.731T>C) can provide a molecular diagnosis in 34.5% of PH1 patients, eliminating the need for a liver biopsy. Having reviewed the distribution of all AGXT mutations, we have evaluated a diagnostic strategy that uses selected exon sequencing for the molecular diagnosis of PH1. METHODS We sequenced exons 1, 4, and 7 for 300 biopsy-confirmed PH1 patients and expressed the identified missense mutations in vitro. RESULTS Our identification of at least 1 mutation in 224 patients (75%) and 2 mutations in 149 patients increased the diagnostic sensitivity to 50%. We detected 29 kinds of sequence changes, 15 of which were novel. Four of these mutations were in exon 1 (c.2_3delinsAT, c.30_32delCC, c.122G>A, c.126delG), 7 were in exon 4 (c.447_454delGCTGCTGT, c.449T>C, c.473C>T, c.481G>A, c.481G>T, c.497T>C, c.424-2A>G), and 4 were in exon 7 (c.725insT, c.737G>A, c.757T>C, c.776 + 1G>A). The missense changes were associated with severely decreased AGT catalytic activity and negative immunoreactivity when expressed in vitro. Missense mutation c.26C>A, previously described as a pathological mutation, had activity similar to that of the wild-type enzyme. CONCLUSIONS Selective exon sequencing can allow a definitive diagnosis in 50% of PH1 patients. The test offers a rapid turnaround time (15 days) with minimal risk to the patient. Demonstration of the expression of missense changes is essential to demonstrate pathogenicity.
Sustainable graywater reuse for residential landscape irrigation – a critical review

The demand for potable water is rising rapidly due to an ever-increasing population, economic activities, and dwindling water supplies. To provide adequate water supplies in the future, understanding the issues and challenges in the reuse of water and developing appropriate strategies for reuse will be critical. One way to augment water supplies for residential use is to reuse graywater – the wastewater from kitchens, bathrooms, and laundries. In this article, we critically review the evolution of water reuse, the definition of graywater, graywater reuse practices, volumes and flow in different situations, and graywater characteristics. We then examine the issues associated with different graywater treatment methods and how using graywater for irrigation around homes affects soil quality and plant growth. The study concludes that graywater treatment costs, human health risks, and its effect on soil quality are some of the challenges that need to be addressed in the future for widespread and sustainable reuse of graywater for irrigation around homes.