Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Systems Biology Peer Review Process File a Dynamic Model of Proteome Changes Reveals New Roles for Transcript Alteration in Yeast Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from the three referees whom we asked to evaluate your manuscript. As you will see from the reports below, the referees find the topic of your study of potential interest. However, they raise substantial concerns on your work, which, I am afraid to say, preclude its publication in its present form. In general, the reviewers appreciated the detailed and rigorous dataset created in this work, and found the topic of potentially broad interest. Nonetheless, they felt that key conclusions based on the modeling analysis remained somewhat weakly supported, and they provide some potential alternate interpretations. While some of these concerns may be addressable with additional discussion, the reviewers clearly indicated that certain issues would require direct experimental testing. The two most important issues appear to be: 1) suppression of protein synthesis after salt treatment needs to be experimentally demonstrated to rule out possible dilution effects (noted by the first reviewer), and 2) the conclusions regarding ribosome redistribution and availability deserve direct testing (indicated strongly by the last reviewer, but also a concern of the first reviewer). The second reviewer also asks for additional discussion regarding the relevance of these results for our understanding of the salt stress response in yeast. In addition, when preparing your revised work please take into consideration the following format and content issues: 1. Please note, that in addition to our capacity to host datasets in our supplementary information section, we provide a new functionality that allows readers to directly download the 'source data' associated with selected figure panels (e.g. <http://tinyurl.com/365zpej>). This sort of figure
Insulin resistance impairs cutaneous wound healing in mice

Obesity is associated with significant changes in skin combined with metabolic alterations such as insulin resistance. Our aim was to investigate the effects of insulin resistance induced by a high‐fat diet on cutaneous wound healing. Male C57BL/6 mice were fed standard chow (SC group) or high‐fat chow (HFC group) for 30 weeks. On day 0 (28th week), an excisional wound was performed. After 14 days (30th week), the mice were euthanized. Starting from the 8th week, the HFC group had a higher body weight. The HFC group became intolerant to glucose, resistant to insulin, and presented increased plasma cholesterol and triglyceride levels. The wound area was greater in the HFC group. The inflammatory infiltrate and the amount of “fibroblast‐like” cells increased in superficial regions of the lesions in the HFC group. The collagen fibers were more organized and denser in the SC group. Hydroxyproline levels were lower in the HFC group. The nitric oxide synthase‐2‐positive cells were higher in the HFC group. Lipid peroxidation and protein carbonyl levels were higher in the HFC group. The expression levels of alpha‐smooth muscle actin and transforming growth factor‐β were higher in the HFC group. These findings support the hypothesis that insulin resistance leads to delayed cutaneous wound healing.
Controlled Markov chains with risk-sensitive criteria: some (counter) examples

The paper is concerned with risk-sensitive versions of the standard average cost and discounted cost criteria for controlled Markov chains. Risk-sensitivity is modelled by means of the family of exponential disutility functions. First, we study the risk-sensitive average cost corresponding to a fixed stationary deterministic policy, for finite state space models. We examine some (counter) examples which illustrate how the behavior of the risk-sensitive model departs from that of the risk-null one in the non-irreducible case. Finally, we present an example of a controlled Markov chain with infinite state space which, as opposed to Jaquette's (1976) result for finite models, does not have ultimately stationary optimal policies with respect to the risk-sensitive (exponential) discounted cost. The controlled Markov chain in that example satisfies a simultaneous Doeblin condition, an assumption that enables the vanishing discount approach in the risk-null models. Thus, the example provides more evidence to think that obtaining the mentioned approach for the risk-sensitive models might be even harder than what Jaquette's result had already indicated.
‘Superior Seedless’ grafted on three selected grapevine rootstocks grown on calcareous soil under diluted brackish water irrigation. I. Growth performances

Mixing brackish water with conventional quality water for irrigation in ratios to maintain satisfactory vigor of grapevines might be a feasible man- agement practice. The objective of this study was to evaluate the performance of three grape rootstocks that are used worldwide and locally; R110, 41B and P1103, irrigated with three salinity levels: 1.5, 3.0 and 5.0 dS m -1 in addition to the 0.8 dS m -1 control. A randomized complete block design was used with three blocks of 12 pots each. ‘Superior Seedless’ grafted on P1103 showed bet- ter performance regarding chlorophyll content, stem length and number of young leaves and even growth after bud break. It does seem that grapevine rootstocks that have either V . rupestris or V . berlandieri in their parentage are good candidates for salinity tolerance. It can be concluded that irrigation with diluted brackish water can be practiced for a certain period of time (two months from April to June); according to our findings under conditions of the experiment , to be followed by irrigation with good quality water in order to flush excessive salts out of the root zone .
The effect of group mindfulness - based stress reduction program and conscious yoga on the fatigue severity and global and specific life quality in women with breast cancer

Background: Cancer is not merely an event with a certain end, but it is a permanent and vague situation that is determined by delayed effects due to the disease, its treatment and its related psychological issues. The aim of this study was to examine the effectiveness of the mindfulness-based stress reduction program and conscious yoga on the mental fatigue severity and life quality of women with breast cancer. Methods: This was a quasi-experimental study with a pre-test, post-test and control group. In this study, 24 patients with the diagnosis of breast cancer were selected among the patients who referred to the Division of Oncology and Radiotherapy of Imam Hossein hospital in Tehran using available sampling method, and were randomly assigned into the experimental and control groups. All the participants completed the Fatigue Severity Scale, Global Life Quality of Cancer Patient and Specific Life Quality of Cancer Patient questionnaires. Data were analyzed by multivariate repeated measurement variance analysis model. Results: Findings revealed that the mindfulness-based stress reduction treatment significantly improved the overall quality of life, role, cognitive, emotion, social functions and pain and fatigue symptoms in global life quality in the experimental group. It also significantly improved the body image, future functions and therapy side effects in specific life quality of the experimental group compared to the control group. In addition, fatigue severity caused by cancer was reduced significantly. Conclusion: The results showed that the mindfulness - based stress reduction treatment can be effective in improving global and specific life quality and fatigue severity in women with breast cancer.
ERG-28 controls BK channel trafficking in the ER to regulate synaptic function and alcohol response in C. elegans

Voltage- and calcium-dependent BK channels regulate calcium-dependent cellular events such as neurotransmitter release by limiting calcium influx. Their plasma membrane abundance is an important factor in determining BK current and thus regulation of calcium-dependent events. In C. elegans, we show that ERG-28, an endoplasmic reticulum (ER) membrane protein, promotes the trafficking of SLO-1 BK channels from the ER to the plasma membrane by shielding them from premature degradation. In the absence of ERG-28, SLO-1 channels undergo aspartic protease DDI-1-dependent degradation, resulting in markedly reduced expression at presynaptic terminals. Loss of erg-28 suppressed phenotypic defects of slo-1 gain-of-function mutants in locomotion, neurotransmitter release, and calcium-mediated asymmetric differentiation of the AWC olfactory neuron pair, and conferred significant ethanol-resistant locomotory behavior, resembling slo-1 loss-of-function mutants, albeit to a lesser extent. Our study thus indicates that the control of BK channel trafficking is a critical regulatory mechanism for synaptic transmission and neural function. DOI: http://dx.doi. org/10.7554/eLife.24733. 001
Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.
THE LIFE‐EXPECTANCY OF PERSONS WITH CEREBRAL PALSY

Survival rates for persons with cerebral palsy were calculated using information front a population‐based registry which has been collecting data since 1952. The 30‐year survival rate approximates 87 per cent. Adverse factors affecting survival are the type of cerebral palsy (spastic quadriplegia having the worst prognosis), epilepsy and severe or profound menial retardation. The length of time over which the data were collected precludes estimating survival time beyond 30 years.
Control Strategies for Self-Adaptive Software Systems

The pervasiveness and growing complexity of software systems are challenging software engineering to design systems that can adapt their behavior to withstand unpredictable, uncertain, and continuously changing execution environments. Control theoretical adaptation mechanisms have received growing interest from the software engineering community in the last few years for their mathematical grounding, allowing formal guarantees on the behavior of the controlled systems. However, most of these mechanisms are tailored to specific applications and can hardly be generalized into broadly applicable software design and development processes. This article discusses a reference control design process, from goal identification to the verification and validation of the controlled system. A taxonomy of the main control strategies is introduced, analyzing their applicability to software adaptation for both functional and nonfunctional goals. A brief extract on how to deal with uncertainty complements the discussion. Finally, the article highlights a set of open challenges, both for the software engineering and the control theory research communities.
H+-Independent Glutamine Transport in Plant Root Tips

Background Glutamine is one of the primary amino acids in nitrogen assimilation and often the most abundant amino acid in plant roots. To monitor this important metabolite, a novel genetically encoded fluorescent FRET-reporter was constructed and expressed in Arabidopsis thaliana. As a candidate for the glutamine fluxes, the root tip localized, putative amino acid transporter CAT8 was analyzed and heterologously expressed in yeast and oocytes. Principal Findings Rapid and reversible in vivo fluorescence changes were observed in reporter-expressing root tips upon exposure and removal of glutamine. FRET changes were detected at acid and neutral pH and in the presence of a protonophore, suggesting that part of the glutamine fluxes were independent of the pH. The putative amino acid transporter CAT8 transported glutamine, had a half maximal activity at ∼100 µM and the transport was independent of external pH. CAT8 localized not only to the plasma membrane, but additionally to the tonoplast, when tagged with GFP. Ultrastructural analysis confirmed this dual localization and additionally identified CAT8 in membranes of autophagosomes. Loss-of function of CAT8 did not affect growth in various conditions, but over-expressor plants had increased sensitivity to a structural substrate analog, the glutamine synthetase inhibitor L-methionine sulfoximine. Conclusions The combined data suggest that proton-independent glutamine facilitators exist in root tips.
Optimal linear filtering under parameter uncertainty

This paper addresses the problem of designing a guaranteed minimum error variance robust filter for convex bounded parameter uncertainty in the state, output, and input matrices. The design procedure is valid for linear filters that are obtained from the minimization of an upper bound of the error variance holding for all admissible parameter uncertainty. The results provided generalize the ones available in the literature to date in several directions. First, all system matrices can be corrupted by parameter uncertainty, and the admissible uncertainty may be structured. Assuming the order of the uncertain system is known, the optimal robust linear filter is proved to be of the same order as the order of the system. In the present case of convex bounded parameter uncertainty, the basic numerical design tools are linear matrix inequality (LMI) solvers instead of the Riccati equation solvers used for the design of robust filters available in the literature to date. The paper that contains the most important and very recent results on robust filtering is used for comparison purposes. In particular, it is shown that under the same assumptions, our results are generally better as far as the minimization of a guaranteed error variance is considered. Some numerical examples illustrate the theoretical results.
Medical and Surgical Readmissions in the Veterans Health Administration: What Proportion are Related to the Index Hospitalization?

Background:Readmissions are an attractive quality measure because they offer a broad view of quality beyond the index hospitalization. However, the extent to which medical or surgical readmissions reflect quality of care is largely unknown, because of the complexity of factors related to readmission. Identifying those readmissions that are clinically related to the index hospitalization is an important first step in closing this knowledge gap. Objectives:The aims of this study were to examine unplanned readmissions in the Veterans Health Administration, identify clinically related versus unrelated unplanned readmissions, and compare the leading reasons for unplanned readmission between medical and surgical discharges. Methods:We classified 2,069,804 Veterans Health Administration hospital discharges (Fiscal Years 2003–2007) into medical/surgical index discharges with/without readmissions per their diagnosis-related groups. Our outcome variable was “all-cause” 30-day unplanned readmission. We compared medical and surgical unplanned readmissions (n=217,767) on demographics, clinical characteristics, and readmission reasons using descriptive statistics. Results:Among all unplanned readmissions, 41.5% were identified as clinically related. Not surprisingly, heart failure (10.2%) and chronic obstructive pulmonary disease (6.5%) were the top 2 reasons for clinically related readmissions among medical discharges; postoperative complications (ie, complications of surgical procedures and medical care or complications of devices) accounted for 70.5% of clinically related readmissions among surgical discharges. Conclusions:Although almost 42% of unplanned readmissions were identified as clinically related, the majority of unplanned readmissions were unrelated to the index hospitalization. Quality improvement interventions targeted at processes of care associated with the index hospitalization are likely to be most effective in reducing clinically related readmissions. It is less clear how to reduce nonclinically related readmissions; these may involve broader factors than inpatient care.
Glucose-induced Remodeling of Intermediary and Energy Metabolism in Procyclic Trypanosoma brucei*

The procyclic form of Trypanosoma brucei is a parasitic protozoan that normally dwells in the midgut of its insect vector. In vitro, this parasite prefers d-glucose to l -proline as a carbon source, although this amino acid is the main carbon source available in its natural habitat. Here, we investigated how l -proline is metabolized in glucose-rich and glucose-depleted conditions. Analysis of the excreted end products of 13C-enriched l -proline metabolism showed that the amino acid is converted into succinate or l -alanine depending on the presence or absence of d-glucose, respectively. The fact that the pathway of l -proline metabolism was truncated in glucose-rich conditions was confirmed by the analysis of 13 separate RNA interference-harboring or knock-out cell lines affecting different steps of this pathway. For instance, RNA interference studies revealed the loss of succinate dehydrogenase activity to be conditionally lethal only in the absence of d-glucose, confirming that in glucose-depleted conditions, l -proline needs to be converted beyond succinate. In addition, depletion of the F0/F1-ATP synthase activity by RNA interference led to cell death in glucose-depleted medium, but not in glucose-rich medium. This implies that, in the presence of d-glucose, the importance of the F0/F1-ATP synthase is diminished and ATP is produced by substrate level phosphorylation. We conclude that trypanosomes develop an elaborate adaptation of their energy production pathways in response to carbon source availability.
Motion background modeling based on context-encoder

A background modeling method for motion-based background of a video made by moving camera is proposed in this paper. We utilize the recently proposed context-encoder to model the motion-based background from a dynamic foreground. This method aims to restore the overall scene of a video by removing the moving foreground objects and learning the feature of its context. An advantage of this method is that the performance of background modeling will not be affected when the camera is moving fast.
From Greece to Norway with Useful Knowledge.

There is a need for a more sustainable diet in many countries. Using Mediterranean principles could provide a possible answer. The principles of the Mediterranean diet and suitability to the Nordic diet have been discussed in courses mainly for Norwegian food and health teachers and students visiting Greece. What benefits do the participants experience after returning home and how do they apply their new knowledge in Norwegian conditions? We studied the themes from the exam papers to find out which knowledge the participants acquired from the course, and how they transferred their knowledge about the Mediterranean diet to Norwegian conditions. We also conducted a survey among the participants; they reported that they felt they benefited from the course. It seems the students are able to translate their knowledge about Mediterranean diet to Norwegian conditions, and the teachers who participated in the course used their knowledge in teaching. Most of the participants use this knowledge in their daily lives.
Still not systematic after all these years: On the compositional skills of sequence-to-sequence recurrent networks

Humans can understand and produce new utterances effortlessly, thanks to their systematic compositional skills. Once a person learns the meaning of a new verb "dax," he or she can immediately understand the meaning of "dax twice" or "sing and dax. " In this paper, we introduce the SCAN domain, consisting of a set of simple compositional navigation commands paired with the corresponding action sequences. We then test the zero-shot generalization capabilities of a variety of recurrent neural networks (RNNs) trained on SCAN with sequence-to-sequence methods. We find that RNNs can generalize well when the differences between training and test commands are small, so that they can apply "mix-and-match" strategies to solve the task. However, when generalization requires systematic compositional skills (as in the "dax" example above), RNNs fail spectacularly. We conclude with a proof-of-concept experiment in neural machine translation, supporting the conjecture that lack of systematicity is an important factor explaining why neural networks need very large training sets.
A problem of a shortage of female managers or a problem of a surplus of male managers

This paper aims to add knowledge about solving stock-flow tasks, in particular in the field of personnel policies, by studying the effect of differences in framing of such a task on performance of subjects Framing is the effect that the formulation of a problem has on ones understanding of and actions towards that problem. Participants in a system dynamics inventory task seem to react differently to a problem when it is formulated in different ways, which in turn might have an effect on the degree of stock-flow failure of the participant. Participants had to perform a variation of the Female Professors task, namely a managers task from a male perspective and a managers task from a female perspective, in which the question asked was the same but the frame of the tasks differed. It appeared that the participants with the managers task from the male perspective recommended on average more extreme numbers in their reasoning than the participants with the managers task from the female perspective. There was no difference in stock-flow failure between the two groups of participants.