Miracle-dz/UniFAR-FTUs huggingface dataset:
Letters to the Editor

As an analyst frequently confronted with sparse tabular data, I read with interest the comparison of maximum-likelihood and exact logistic regression (MLR and ELR) by King and Ryan (2002), who noted the superiority of ELR to MLR in the contexts they examined. There are important alternatives to these methods,however. In particular, according to some criteria, frequentist shrinkage estimators (such as empirical-Bayes estimators), Bayes estimators, and “semiBayes” hybrids can exhibit much better small-sample performance and produce contextually more sensible results than either MLR or ELR, even in problems with few parameters. The poor behavior of unconditionalMLR in small samples and sparse data has long been known (Pike, Hill, and Smith 1980), and similar problems have also been noted in conditionalMLR (Greenland 2000a,b;Greenland, Schwartzbaum, and Finkle 2000). Unfortunately, in terms of failing to provide sensible answers, ELR sometimes does just as poorly as MLR (Greenland et al. 2000). For a Bayesian, at least, the reason is clear: Classical methods like MLR and ELR neglect prior information, which becomes crucial in small-sample problems (Winkler 2002; Winkler, Smith, and Fryback 2002). The corresponding frequentist point is that certain aspects of small-sample performance can be greatly improved by intelligent shrinkage of estimators. Both points were made long ago in the contingency-tablecontext (Bishop, Feinberg, and Holland 1975,chap. 14; Good 1965) and have been extended to general nonlinear regression by modern theory (e.g., Carlin and Louis 2000). I recently examined these issues in epidemiologic contexts akin to King and Ryan’s biomedical examples (Greenland 2000a,b; Greenland et al. 2000), and suggested that epidemiologic analyses would usually be better served by even the simplest shrinkage methods than by exact methods or approximations to the latter (Greenland 2000b, 2001). In part, this is because the epidemiologic contexts in which any of this matters are those in which the effects under study are already known to be not far from zero, so shrinkage toward zero can help frequency properties immensely, and corresponds to use of a reasonable prior distribution. I strongly suggest that future comparisons of logistic (and other) regression techniques routinely include various shrinkage methods among the candidates, and also give some consideration to contextually sensible loss functions (not just squared-error loss or the loss functions implicit in a 0.05-level test of the null hypothesis).
Slowly activating vacuolar channels can not mediate Ca2+-induced Ca2+ release

In order to test the hypothesis that slowly activating vacuolar (SV) channels mediate Ca2+-induced Ca2+ release the voltage- and Ca2+-dependence of these K+ and Ca2+- permeable channels were studied in a quantitative manner. The patch-clamp technique was applied to barley (Hordeum vulgare L.) mesophyll vacuoles in the whole vacuole and vacuolar-free patch configuration. Under symmetrical ionic conditions the current-voltage relationship of the open SV channel was characterized by a pronounced inward rectification. The single channel current amplitude was not affected by changes in cytosolic Ca2+ whereas an increase in vacuolar Ca2+ decreased the unitary current in a voltage-dependent manner. The SV channel open-probability increased with positive potentials and elevated cytosolic Ca2+, but not with elevated cytosolic Mg2+. An increase of cytosolic Ca2+ shifted the half-activation potential to more negative voltages, whereas an increase of vacuolar Ca2+ shifted the half-activation potential to more positive voltages. At physiological vacuolar Ca2+ activities (50 μM to 2 mM) changes in cytosolic Ca2+ (5 μM to 2 mM) revealed an exponential dependence of the SV channel open-probability on the electrochemical potential gradient for Ca2+ (ΔμCa). At the Ca2+ equilibrium potential (ΔμCa = 0) the open-probability was as low as 0.4%. Higher open-probabilities required net Ca2+ motive forces which would drive Ca2+ influx into the vacuole. Under conditions favouring Ca2+ release from the vacuole, however, the open-probability further decreased. Based on quantitative analysis, it was concluded that the SV channel is not suited for Ca2+-induced Ca2+ release from the vacuole.
Oxytocinase: Placental Cystine Aminopeptidase or Placental Leucine Aminopeptidase (P-LAP)

Previously it was believed that peptide hormones such as oxytocin, vasopressin, and angiotensin pro­ duced in the maternal sites played important roles in the physiology and pathology of pregnancy. How­ ever, recent advances in fetal endocrinology suggest that peptide hormones derived from the fetal site are more important than those from the maternal site in the physiology and pathology of human pregnancy. It is known that human fetuses produce high levels of oxytocin that increase with the advancement of gestation, increased quantities of vasopressin with fetal acidosis, and increasing amounts of angioten­ sin accompanying fetal growth and/or fetal acid­ emia. Since oxytocin is known to be a potent uterotonic agent, and vasopressin and angiotensin to be potent vasoactive ones, an increase of these hor­ mones in the fetus may have an important effect on the uterine tonus and/or uteroplacental blood flow. It is reasonable to speculate, therefore, that enzymes exist that metabolize and degrade these hormones in the pregnant serum and the placenta.
Comment

Exploring a possible correlation between the efficient price and the noise, as HL do, is an exciting and challenging task. By examining the volatility signature plots of trades and quotes, HL report that realized variance (RV) estimates based on quotes at very high frequency decrease. This is different from many earlier findings on volatility signature plots based on transaction prices. It is important to figure out how much of that is driven by the preprocessing of the data of HL, and we discuss the role that this might have played in delivering that result. A different issue is that volatility signature plots give us a point estimate of RV at different sampling frequencies. A substantial increase or decrease of RV at high sampling frequencies can signify an upward bias or downward bias. But what magnitude of change in RV is large enough to be considered a signal for bias? This can be answered by superimposing the pointwise interval estimates of RV on the original plot. It seems that HL attempt to address this issue by providing a 95% confidence band of RV tick) ACNW30 . However, the 95% confidence band that they provide, seems to represent the variation between ask, bid, and trades, rather than displaying the uncertainty in the estimator RV tick) ACNW30 itself. In other words, we do not know whether or not the dipping at the higher sampling frequency in HL’s figure 1 is statistically significant. We know that the inconsistent estimator RV tick) ACNWk would have a nonnegligible bias and stochastic term, and thus the pointwise confidence intervals could be quite wide. We explore this further here (see Table 1). We also explore the connection between this finding and the identifiability, or lack thereof, of certain noise models.
Operationalizing the actualizing tendency

ABSTRACT The actualizing tendency is the basis of person-centered therapy. The therapist’s use of congruence, unconditional positive regard, and empathy is assumed to facilitate the client’s access to this natural predilection for fulfilling one’s potential. There are no criteria for how this happens. There are two likely reasons: (a) no consensus on how these conditions are understood, and therefore to be used, and (b) no effective method for handling the major obstacle for accessing this tendency: The residual effects of hurtful psychological experiences. The proposed method is this author’s concept of therapeutic catharsis, and which is also offered as a falsifiable conceptualization of the actualizing tendency. The facilitative condition for therapeutic catharsis is the unforced activation of the client’s emotional experiencing; i.e. it arises coincident with clients receiving sufficient support for their experiencing. The core therapeutic conditions, understood as follows, establish this condition: Unconditional positive regard is the unqualified acceptance of the client’s experiencing; empathy is for understanding the explicit and implicit dimensions of the client’s experiencing; and the therapist’s congruent behaviour is the delivery system for both
Experimental investigation on mahua methyl ester blended with diesel fuel in a compression ignition diesel engine

In this article, the mahua tree’s high importance in the present-day plantations is described and the preparation of mahua methyl ester (MME) from the raw mahua seed oil by the two methods of the transesterification process is described. The tested physical properties were compared with the requirement of ASTM D-6751. The obtained MME and its blends of B20, B40, B60, and B80 were investigated in an unmodified diesel engine. From the results of the performance, it has been observed that brake-specific fuel consumption and brake thermal efficiency are slightly improved (B20 and B40) at part-load conditions and approach diesel at full-load conditions. From combustion analysis, it was seen that ignition delay was shorter for biodiesel and its blends compared with the diesel fuel. The emission characteristics of carbon monoxide, hydrocarbons, and smoke opacity were reduced for all the fuel blends, but at high temperatures they undergo an endothermic reaction and produced various oxides of nitrogen.
COMPETITIVE INTERACTIONS BETWEEN TREE SPECIES IN NEW ZEALAND'S OLD‐GROWTH INDIGENOUS FORESTS

New Zealand's four broad-leaved evergreen tree species from the genus Nothofagus all show pronounced distributional disjunctions, independent of environmental factors known to influence tree distributions. Here, we use these disjunctions as the basis for a natural removal experiment to investigate competitive interactions between Nothofagus and a range of other widespread conifer and broad-leaved tree species. We first model the abundance of non-Nothofagus species as a function of environment, using Generalized Additive Models (GAMs) and an extensive data set sampling much of New Zealand's remaining old-growth forests. We then assess the effects of competitive interaction with Nothofagus by adding statistical terms describing (1) Nothofagus abundance, and (2) interactions between Nothofagus abundance and annual temperature, the dominant environmental gradient. Results indicate substantial reductions in the abundance of many species as Nothofagus abundance increases. The magnitude of this reduction varies with position along the dominant environmental gradient; species overlapping most strongly with Nothofagus are generally most sensitive to increases in Nothofagus abundance. In addition, both the shapes of species responses to mean annual temperature and the positions of their optima change as Nothofagus abundance increases. This demonstration of competition using community compositional data has implications both for vegetation theory and for prediction of the likely impacts of global warming on New Zealand's forest pattern.
Seasonal variations of epilithic diatoms on different hard substrates, in the northern Adriatic Sea

The colonization of epilithic diatoms on artificial hard substrates (marble, quartzite and slate) was investigated on a seasonal basis in a subtidal site of the northern Adriatic Sea to determine if substrate-dependent differences in colonization occurs and to define the seasonal variations of microepilithic communities in terms of abundance, biomass and community structure. Artificial substrates (smoothed small discs mounted on a Plexiglas sheet) were placed at a depth of 8 m in April 2003, July 2003, January 2004 and February 2004. The discs were collected after 6–7 weeks for counting and taxonomic identification of the diatoms. The community structure of epilithic diatoms showed a dominance of motile species over the entire study period, followed by erect, adnate and tube-dwelling diatoms. Diatom density showed a marked seasonal variability, ranging from 365±407 (winter 2004) to 557156±82602 cells cm-2 (spring 2004). Biomass ranged from 0.02±0.01 to 17.53±3.20 μg C cm-2. Abundance and biomass values did not present any significant differences for the three substrates examined.
Who captures the “green value” in the US office market?

This research examines the effects of energy efficiency certification levels on office rental rates and lease structures to determine whether any cost benefits of green buildings are captured by landlords or remain, at least partially, with the tenant. To this aim, our analysis applies the largest and most detailed data set to date, a panel of 14,283 US office properties. Using fixed-effects and dynamic Arellano–Bond frameworks allows us to estimate the differential rental price impact of Energy Star certification both across and within buildings. The general results indicate that buildings with higher levels of energy efficiency achieve higher gross rents allowing landlords to benefit from the premium. However, improved energy efficiency over time is also linked to a slower growth of rental prices as some of the benefit is passed onto tenants. Interestingly, the cost-saving benefit of energy efficiency appears to have the strongest impact on rental rates.
Effect of chemical composition and thermal properties on the cooking quality of common beans (Phaseolus vulgaris)

The relationship between chemical composition and thermal properties as it affects the degree of cooking in six varieties of common beans was investigated. The degree of cooking (DC) and the hardness of cooked beans were estimated by differential scanning calorimetry (DSC) and texture analysis, respectively. The total protein of bean seeds varied between 19.7 and 23.6%. However, the fractions of albumin, glutelin, and globulin showed significant differences among varieties. The amylose content varied from 18.4 to 36.0%. The first endothermic peak was associated with inactivated enzymatic activity, denaturation of low-protein fractions, and starch gelatinization, while the second endothermic peak was associated with the denaturation of heat-resistant protein fractions. The high values of minerals and chemical composition among bean varieties affected thermal behavior and was associated with greater hardness and a lower degree of cooking.
Examination of antimicrobial potential in natural isolates of lactobacillus casei/paracasei group

The aim of this study was to investigate the antimicrobial potential of 52 natural isolates of Lactobacillus casei/paracasei. The incidence of relevant genes encoding BacSJ (bacSJ2-8/bacSJ2-8i gene cluster), acidocin 8912 (acdT), ABC-transporter (abcT) and accessory protein (acc) was also studied. These genes were found to be widespread amongst the analyzed L. casei/paracasei strains. The bacSJ2-8/bacSJ2-8i gene cluster was present in 49 (94.23%) and acdT in 41 (78.85%) of the 52 tested strains. Forty of these strains (76.92%) harbored both analyzed genes. Interestingly, only 17 strains (32.69%) with the bacSJ2-8/bacSJ2-8i gene cluster and/or the acdT gene showed bacteriocin production. Strain L. paracasei BGNK1-62 contained the bacSJ2-8/bacSJ2-8i gene cluster, but did not produce bacteriocin BacSJ possibly due to absence of the abcT and acc genes. Hence, these genes were introduced into BGNK1-62 by transformation with constructed plasmid pA2A, after which BacSJ was produced. In addition, it was found that L. paracasei BGGR2-66 produced new bacteriocin designated as BacGR that was biochemically characterized and its N- terminal sequence was determined. [Projekat Ministarstva nauke Republike Srbije, br. 173019]
Comment

We would like to congratulate the authors of this article on a thoughtful and thorough design and data analysis. Their analysis represents a good example of how complex longitudinal data from observational studies or randomized trials should be analyzed, and reflects care and thought. The authors target questions of interest using sophisticated causal inference tools instead of allowing available software and common practice to dictate the analysis.
An Empirical Analysis of Capital Structure and Firm’s Financial Performance in a Developing Country

This paper aims to empirically study the relationship between capital structure and firm’s financial performance in a developing country like Bangladesh. The investigation has been conducted through using panel data procedure for a sample of Dhaka stock market enlisted all IT firms during the year of 2013-2017. This research works have been performed through the three performance measures including return on equity, return on asset, and earnings per share as dependent variables, where capital structure is considered as debt ratio (DR), equity ratio (ER), long-term debt ratio (LTDR), short-term debt ratio (STDR) and used as independent variables. However, descriptive statistics, correlation, pooled ordinary least square analysis, fixed effect and Random effect model has been analyzed to find the relationship between capital structure and financial performance.
Solar UV‐B radiation affects below‐ground parameters in a fen ecosystem in Tierra del Fuego, Argentina: implications of stratospheric ozone depletion

Stratospheric ozone depletion caused by the release of chlorofluorocarbons is most pronounced at high latitudes, especially in the Southern Hemisphere (including the so‐called ‘ozone hole’). The consequent increase in solar ultraviolet‐B radiation (UV‐B, 280–315 nm) reaching the earth's surface may cause a variety of alterations in terrestrial ecosystems. Most effects might be expected to occur above‐ground since sunlight does not penetrate effectively below‐ground. Here, we demonstrate that solar UV‐B radiation in a fen in Tierra del Fuego (Argentina), where the ozone hole passes overhead several times during the Austral spring, is causing large changes of below‐ground processes of this ecosystem. During the third and fourth year of a manipulative field experiment, we investigated root systems in these plots and found that when the ambient solar UV‐B radiation was substantially reduced, there was a 30% increase in summer root length production and as much as a threefold decrease in already low symbiotic mycorrhizal colonization frequency of the roots compared with plots receiving near‐ambient solar UV‐B. There was also an apparent shift toward older age classes of roots under reduced solar UV‐B. Such large changes in root system behaviour may have decided effects on competition and other ecological interactions in this ecosystem.
Diversity of macrofungi and exploitation of edible mushroom resources in the National Park “Appennino Lucano, Val D'Agri, Lagonegrese” (Italy)

An investigation on the macrofungal diversity of the National Park “Appennino Lucano, Val D'Agri, Lagonegrese” (Basilicata, southern Italy) was carried out, together with an evaluation of wild edible mushrooms in agro-forest ecosystems and their possible exploitation as a new source of food and revenue in rural and under-developed areas of this region. An unpublished list of 249 mushroom taxa (229 Basidiomycota and 20 Ascomycota), mostly belonging to the genera Tricholoma, Tuber, Russula, Amanita, Boletus, Lactarius, Mycena, Agaricus, Clitocybe and Hygrophorus, growing in this important natural area is provided together with ecological characterization of the recorded specimens. Inonotus obliquus is a new record for Basilicata, while Mycena bresadolana is reported for the first time from southern Italy. The presence of Amaurodon mustialaënsis, an extremely rare species of the northern hemisphere reported for the first time on white fir, is noteworthy. Among the previous findings, 116 species of edible mushrooms are presented and discussed in view of their relative abundance and edibility.
Comment

be consistent for some functional of the assumed model. It is not clear whether this population quantity will be easily accessible and interpretable, in general (especially, outside a specific model), but it might be reasonable in the multivariate location– scale situation. However, this will certainly require extensive comparisons with other depth measures and other robust approaches. In summary, at present traditional data depth looks more straightforward to us for exploratory data analysis. Although the work here suggests the exciting possibility that likelihoodbased parameter depth might also prove useful in a diagnostic mode (in addition to providing robust parameter estimates), we feel that these implications still need to be drawn more completely. In general, the distinction between data depth and parameter depth seems quite important. Should we say that data depth is traditional fare and parameter depth is the genetically engineered variety? We do not know yet which one will dominate the future supermarket, but for now it seems clear that both will be on the shelves.
Differential effects of p19Arf and p16Ink4a loss on senescence of murine bone marrow-derived preB cells and macrophages

Establishment of cell lines from primary mouse embryo fibroblasts depends on loss of either the Arf tumor suppressor or its downstream target, the p53 transcription factor. Mouse p19Arf is encoded by the Ink4a-Arf locus, which also specifies a second tumor suppressor protein, the cyclin D-dependent kinase inhibitor p16Ink4a. We surveyed bone marrow-derived cells from wild-type, Ink4a-Arf-null, or Arf-null mice for their ability to bypass senescence during continuous passage in culture. Unlike preB cells from wild-type mice, those from mice lacking Arf alone could be propagated indefinitely when placed onto stromal feeder layers engineered to produce IL-7. The preB cell lines remained diploid and IL-7-dependent and continued to express elevated levels of p16Ink4a. By contrast, Arf-null bone marrow-derived macrophages that depend on colony-stimulating factor-1 for proliferation and survival in culture initially grew at a slow rate but gave rise to rapidly and continuously growing, but still growth factor-dependent, variants that ceased to express p16Ink4a. Wild-type bone marrow-derived macrophages initially expressed both p16Ink4a and p19Arf but exhibited an extended life span when p16Ink4a expression was extinguished. In all cases, gene silencing was accompanied by methylation of the Ink4a promoter. Therefore, whereas Arf loss alone appears to be the major determinant of establishment of murine fibroblast and preB cell lines in culture, p16Ink4a provides an effective barrier to immortalization of bone marrow-derived macrophages.
Comment

I congratulate the authors for their excellent contribution covering practical and nonstandard mathematical aspects of inference. Quantifying uncertainty belongs to the core of statistics. The standard (and overly simplified) measure for classification accuracy is an estimated test set or generalization error. Laber and Murphy address a much more appropriate and more challenging task: constructing accurate confidence intervals for the test set error. I very much agree with them that quantifying accuracy should be pursued with measures taking uncertainty into account. Laber and Murphy present thorough mathematical analysis and arguments showing that with small sample size, the asymptotic framework should be chosen carefully. I concur with their views and mathematical argumentation. In what follows, I attempt to make a few selective cross-connections to related issues that have been worked out in the past.