Miracle-dz/UniFAR-FTUs huggingface dataset:
Reviewers ' Comments : Reviewer # 2 : None

Reviewer #1: Remarks to the Author: This study makes comparisons of fish communities between two gulfs and finds them to be different. It then inappropriately attributes these differences to differences in temperature regimes between the two locations. Two communities can differ for any number of reasons, temperature is just one. To conclude, on the basis of comparing just two sites, that temperature is the principal driver (from the Abstract: "Rather, impoverished body conditions of 35 populations in the Arabian Gulf point toward an increased energetic costs of growth and 36 homeostasis at higher temperatures). The scale at which the factor of interest varies here is "Gulf", consequently the unit of replication to make valid inferences is also "Gulf". The study does not replicate at that scale and so none of the inferences are supported. I recognise that replicating at that scale would be challenging but consider that that the statement that the authors is making is substantial that temperature is the most important driver of differences among gulf to make a substantive statement requires substantive evidence. There is vast literature on making comparisons across large spatial scales such as the one proposed here, particularly protected area studies on both land and sea. Likewise, there is a large body of work on local adaptation of physiology (Conover in fish is a good exemplar). This work does not approach this problem at the appropriate scale and does no provide sufficient support for any of the key inferences. I'm sorry I cannot be more positive but for work to be published in a high impact journal, best practice in terms of experimental design is essential.
Bacterial endophytes in cotton: mechanisms of entering the plant

Investigations were conducted to determine how a systemic plant-colonizing bacterium Enterobacter asburiae JM22 enters cotton plant tissues. Passive uptake was excluded for JM22 by experimentation with glutaraldehyde-fixed (killed) bacterial cells applied to seeds and leaves; no bacteria were found internally or externally on roots or leaves. In contrast, application of live JM22 cells led to colonization of external and internal root and leaf tissues. Active penetration of JM22 in the absence of external wounding was demonstrated for cotton seedlings germinated on water agar and inoculated with the bacterial suspension. The mean internal bacterial population density for seedlings was 3.8 x lo3 CFUIg surface-disinfected radicle tissue. Studies of in planta enzymatic activity demonstrated hydrolysis of wall-bound cellulose in the vicinity of JM22 bacterial cells. The same phenomenon was observed for a cortical root colonizing bacterium, Pseudomonas fluorescens 89B-61, a plant growth-promoting strain with biocontrol potential against various pathogens.
AFLNET: A Greybox Fuzzer for Network Protocols

Server fuzzing is difficult. Unlike simple command-line tools, servers feature a massive state space that can be traversed effectively only with well-defined sequences of input messages. Valid sequences are specified in a protocol. In this paper, we present AFLNET, the first greybox fuzzer for protocol implementations. Unlike existing protocol fuzzers, AFLNET takes a mutational approach and uses state-feedback to guide the fuzzing process. AFLNET is seeded with a corpus of recorded message exchanges between the server and an actual client. No protocol specification or message grammars are required. AFLNET acts as a client and replays variations of the original sequence of messages sent to the server and retains those variations that were effective at increasing the coverage of the code or state space. To identify the server states that are exercised by a message sequence, AFLNET uses the server’s response codes. From this feedback, AFLNET identifies progressive regions in the state space, and systematically steers towards such regions. The case studies with AFLNET on two popular protocol implementations demonstrate a substantial performance boost over the state-of the-art. AFLNET discovered two new CVEs which are classified as critical (CVSS score CRITICAL 9.8).
Production of Acidic protease using Submerged Fermentation by Rhizopus arrhizus

The study is concerned with utilize whey of milk factory as a carbon source for the production of protease. The project was planned to produce maximum protease from whey by Rhizopus arrhizus at pH 4 and 37 °C temperature. Growth media employed to culture Rhizopus arrhizus for the production of enzyme were developed and fermentation conditions was optimized through various trials. Substrate water ratio, different nitrogen sources and concentration of nitrogen source were optimized. The fermented materials were harvested after 72 hours. These were filtered and centrifuged at 10,000 rpm at -10 °C. The filtrates were subjected to enzyme assay. Absorbance of the enzyme sample was determined at 700 nm on spectrophotometer. It was observed that 90% Whey and 2.5% cotton seed meal enhanced the production of protease by Rhizopus arrhizus . Maximum enzyme activity was observed (149.26 IU/ml/min) in flask level at pH 4 and 37 °C temperature. These optimized conditions of growth media was again used in Air-Lift fermenter and determined the activity (169.78 IU/ml/min) that is greater than flask level. This is due to proper aeration and proper temperature in Air-lift fermenter. Keywords: Acidic protease, Air-lift fermentor, submerged fermentation and Rhizopus arrhizus
Loading Human Mesenchymal Stem Cells with Trehalose by Fluid-Phase Endocytosis

Human mesenchymal stem cells (MSCs) have shown great promise in the area of tissue engineering. Regardless of their regenerative potential, however, they will not be useful on a large scale unless an improved and more stable form of cellular storage is developed. An ideal storage condition would be dehydrated cells, as this would allow room temperature storage and would not require refrigeration or freezing equipment. As a first step toward developing a method for storing MSCs in a desiccated state, we have characterized the ability of these cells to take up solutes from the extracellular milieu, as the introduction of protective solutes into the cytosol is a critical step in the dehydration process. Lucifer yellow (LYCH), a well-known probe in the study of fluid-phase endocytosis, indicated the uptake process was inhibited below 20°C. Fourier transfer infrared spectroscopy studies suggested that this inhibition is associated with the membrane physical state. In addition, fluorescence microscopy revealed .
Challenges and opportunities to the African agriculture and food system

Reduction in the proportion of undernourished people worldwide has been achieved despite global population increase. However, the achievement of reducing undernourishment globally was uneven; sub-Saharan Africa (SSA) in particular has the least progress. In SSA, agriculture is only slowly changing with actual well below potential yields. Failures in agricultural policies, weak institutions, and poor governance are the root of growth stagnation. Agriculture contributes a significant share to the SSA economy and a majority of the population derives their livelihood from this sector. It is justifiable to assume that for sustainable growth of the African economy, significant investment and creative innovation in agriculture are needed. However, several factors such as growth of the farming population, loss of soil fertility, climate change, water scarcity, post-harvest losses, and limited market access could challenge such expectation. On the other hand, new policy reforms and initiatives, and appropriate investment that directly or indirectly support agricultural innovation and growth are emerging. This chapter discusses the challenges and opportunities to advance agricultural growth and food systems in Africa and makes recommendations for solutions. Keywords: Africa, food systems, agriculture, agricultural research, agricultural investment
The effects of supplementing an organic acid blend and/or microbial phytase to a corn-soybean based diet fed to broiler chickens

This experiment was designed to investigate the effects of supplementation with phytase, either alone or in combination with an organic acid blend on growth performance, some internal organs measurements and tibia development, intestinal and cecal microbiology. One-day-old male Ross 308 strain broiler chickens (n=140) were allocated to 5 dietary treatments in a randomized complete block design. The treatments were as follows: (1) Positive control (PC); (2) Negative control (NC) that was the same as diet PC except that available phosphorus was reduced by 0.25 percentage units; (3) NC plus microbial phytase (MP) (NC + MP; 500 FTU/kg); (4) NC plus organic acid blend (OA) (NC + OA), and (5) NC + MP + OA. Body weight gain (BWG) was not improved by supplementation of OA to the NC diet. In contrast, BWG was increased by MP, and MP+OA interaction (P<0.001) compared to NC group. Tibia ash content was lowest (P<0.05) for birds fed the all NC diets compared to the PC and NC+P diet. The addition of phytase slightly increased tibia phosphorus according to NC+OA and NC+P+OA diets (P<0.05). NC diet resulted in increased weight of gizzard, heart, liver and bursa of Fabricious and length of duodenum, jejunum and ileum. In ileal digesta, lactic acid bacteria (LAB) counts were significantly increased for birds fed OA, whereas Escherichia coli were significantly decreased compared to PC group (P<0.001).
An Efficient Design for a Ranked Search of Multi-keywords in Encrypted Cloud

-The data which is sensitive has an imperative need to be encrypted so as to avoid pruning eyes, which antiquate data driven algorithms such as keyword-based retrieval of required documents. The Secure ranked search of multi-keywords scheme which is implemented on the cloud data which is encrypted, which synchronously has the ability to support update operations such as insertion, deletion dynamically of documents. The kNN algorithm which is secure has been used to as to encrypt various vectors such as the index vector and query vector, on top of this they also ensure calculation of scores between index vectors and query vectors which is encrypted. For the purpose of protecting the vulnerabilities of statistical attacks, certain phantom terms are necessarily added to the existing index vector for the purpose of blinding of the search results. Since we have used a special structure of a tree-based indexing, this design can accomplish the efficiency of linear search and it can additionally deal with insertion and deletion of the required documents in a really flexibly and dynamic way. Comprehensive experimental conditions have been simulation to denote the competence of this particular scheme.
Abstract 5186: A new mode of integrin–Ecadherin cross talk that modulates invasion and metastasis

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Cellular interactions with the extracellular matrix (ECM) are mediated by transmembrane receptors of the integrin family. These interactions coordinate signal transduction cascades impinging on cell survival, proliferation, and migration. Ablation of the β1 integrin gene attenuates initiation and growth of breast and skin cancers and β1 antibodies sensitize breast tumors in mice to radiotherapy. However, the role of β1 integrins in breast cancer progression from a localized tumor to metastatic disease is unknown. We show that peptide blocking or gene silencing of β1 integrins can cause a shift from cohesive multicellular strand invasion to individual cell migration, which acts pro-metastatic in breast cancer cells. While tumor growth of β1 integrin-depleted breast cancer cells is reduced, intravasation and lung metastasis of cells from these small tumors in an orthotopic mouse model is dramatically enhanced, as is migration in a zebrafish xenograft model. Depletion of β1 integrins alters the balance between miR-200 miRNAs and ZEB transcriptional repressors leading to a transcriptional downregulation of E-cadherin, which is essential for the induction of individual cell migration and enhanced metastasis. These findings demonstrate that disturbed integrin-mediated interactions with the ECM in cancer cells can alter cell migration strategies and metastatic potential through a miRNA-transcription factor network that controls cell-cell adhesion. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5186. doi:1538-7445.AM2012-5186
Efficacy of Intravenous Ustekinumab Reinduction in Patients With Crohn’s Disease With a Loss of Response

Abstract Background/Aims In patients receiving ustekinumab (UST) for treatment of Crohn’s disease, there is no proven strategy to enhance or re-capture response. We assessed the utility of UST intravenous (IV) reinduction (~6 mg/kg) to achieve clinical, biochemical and endoscopic response or remission, in patients with partial or loss of response to UST maintenance therapy. Methods A multicentre, retrospective cohort study was performed. Adults who received an IV reinduction dose of UST for either partial response or secondary loss of response to UST were assessed. The primary outcome was clinical remission off corticosteroids (Harvey Bradshaw Index <5), with biochemical response (defined as ≥ 50% decrease of CRP or FCP and/or endoscopic response (defined as a decrease in Simple Endoscopic Score-CD ≥ 50%). Secondary outcomes included clinical, biomarker and endoscopic response/remission, as well as safety. Results Sixty-five patients (median age 38 years, 54.7% women) underwent IV UST reinduction between January 2017 and April 2019. Most patients (88.3%) were already on escalated maintenance dosing of UST 90 mg subcutaneous every 4 weeks. Clinical outcomes were assessed at a median of 14 weeks (IQR: 12–19) post-reinduction. The primary outcome of clinical remission off corticosteroids with biochemical and/or endoscopic response was achieved in 31.0% (n = 18). Pre-reinduction UST concentrations were ≥1 μg/mL in 88.6% (mean 3.2 ± 2.0 μg/mL). No serious adverse events were reported. Conclusions UST IV reinduction can be effective in patients with Crohn’s disease with partial or loss of response to UST maintenance therapy. Further studies evaluating this strategy are warranted.
Surgical Management of Laryngeal and Hypopharyngeal Cancer in a Tertiary Care Centre

Background: Despite advances in techniques and dose regulation of chemoradiotherapy, surgery still plays great role in treating large fraction of well selected locally advanced laryngeal and hypopharyngeal carcinoma. Materials and Methods: A retrospective study of 210 cases of surgically treated laryngeal and hypopharyngeal carcinomas from 2014 to 2015 was analysed. Results: The most common sub site of involvement was hypopharynx (53.3%) followed by glottis (24.7%), supraglottis (15.7%), transglottic malignancy (4.7%), subglottis (0.95%), and for medullary carcinoma of the thyroid (0.47%) respectively. Total laryngectomy was carried out for 162 patients, 180 0f them required Modified radical neck dissection along with laryngectomy. Near total laryngectomy was done in 28 cases. Post-operative hospital stay was for an average of 14 days (range 10-33) after surgery. Histopathologically squamous cell carcinoma was the most common and 2 patients had spindle cell tumour. 180 patients were referred for adjuvant therapy with RT and of which 120 received both chemotherapy and radiotherapy and 60 defaulted from adjuvant therapy. Recurrences were noted both locoregionally and distant in 13.3% of cases. The mean follow up period was 15 months ranging from 2 months to 25 months. Conclusion: Surgical modality as definitive treatment in well selected Indian population with locally advanced stage III and IV laryngeal and hypopharyngeal carcinomas, with adjuvant therapy when indicated, is a valuable option with less complications and morbidity achieving acceptable locoregional control. A regular follow up is warranted to detect the early locoregional and distant failures.
Regulatory Role of γδ T Cells in the Recruitment of CD4+ and CD8+ T Cells to Lung and Subsequent Pulmonary Fibrosis1

The mechanisms by which T cells accumulate in the lungs of patients with pulmonary fibrosis are poorly understood. Because the lung is continually exposed to microbial agents from the environment, we repeatedly exposed C57BL/6 mice to the ubiquitous microorganism, Bacillus subtilis, to determine whether chronic exposure to an inhaled microorganism could lead to T cell accumulation in the lungs and subsequent pulmonary fibrosis. C57BL/6 mice repeatedly treated with B. subtilis for 4 consecutive weeks developed a 33-fold increase in the number of CD4+ T cells and a 354-fold increase in γδ T cells in the lung. The γδ T cells consisted almost entirely of Vγ6/Vδ1+ cells, a murine subset bearing an invariant TCR the function of which is still unknown. Treatment of C57BL/6 mice with heat-killed vs live B. subtilis resulted in a 2-fold increase in the number of CD4+ T cells in the lung but no expansion of γδ T cells indicating that γδ cells accumulate in response to live microorganisms. In addition, mice treated with heat-killed B. subtilis developed significantly increased pulmonary fibrosis compared with mice treated with the live microorganism. Mice deficient in Vγ6/Vδ1+ T cells when treated with B. subtilis had a 231-fold increase in lung CD4+ T cells and significantly increased collagen deposition compared with wild-type C57BL/6 mice, consistent with an immunoregulatory role for the Vγ6/Vδ1 T cell subset. These findings indicate that chronic inhalation of B. subtilis can result in T cell accumulation in the lung and fibrosis, constituting a new model of immune-mediated pulmonary fibrosis.
Changes in physico-chemical quality characteristics of maize germ during storage

The present study was undertaken to see the effect of different packaging material on physico-chemical quality parameters of maize germ during storage. Maize germ is an enriched by product of starch processing industry and a copious source of oil of good quality. In the pursuance of the study, the germ was extracted at optimum parameter using laboratory size maize degermer machine (at PAU, Ludhiana). The germ was dried to the desired moisture content using mechanical drier and packed in LDPE, HDPE and plastic jar for 60 days under ambient conditions. Different quality parameters viz., color, moisture, fat, protein, fiber, free fatty acid (FFA) and titrable acidity (TA) were determined at regular interval of 15 days for 60 days of storage. Results showed that the maximum germ retained was on sieve size of 1.4 mm with 82.29% retention, average particle size of 1.85+. 01 mm with uniformity index of 1.465: 8.514: 0.017. Statistical analysis showed that all the quality parameters increased significantly (P<0.05) with the increase in the storage period. Further, the moisture, fat, ash, FFA, Fiber increased significantly (P<0.05) whereas protein, fat, TA showed no significant difference (P<0.05) storage period for the combined effect of packaging material and storage period. It was observed that the maize germ stored in HDPE package was found best in quality followed by LDPE and Plastic jar.
Combining Cost-Sensitive Classification with Negative Selection for Protein Function Prediction

Motivation: Computational methods play a central role in annotating the functions of large amounts of proteins delivered by high-throughput technologies. Despite the encouraging results achieved by these methods, many functions still have a very low number of verified protein annotations, leading to a pronounced imbalance between annotated and unannotated proteins. Furthermore, functional taxonomies rarely report negative annotations. This leaves ill defined the set of negative examples, which is crucial for training the majority of machine learning methods. In practice, neglecting data imbalance and the problem of selecing negative examples can strongly limit the accuracy of protein function prediction. Results: We present a novel approach combining a suitable imbalance-aware classification strategy, addressing the scarcity of annotated proteins, with an active learning strategy for selecting the most reliable negative examples. When implemented in a Support Vector Machine, this combined approach shows improved accuracy on yeast and human proteomes over standard SVM and top-performing function prediction tools
Effect of diammonium phosphate application on strigolactone production and Striga hermonthica infection in three sorghum cultivars

Summary Striga hermonthica infection poses a major constraint to sorghum production in sub-Saharan Africa, and low soil fertility aggravates the S. hermonthica problem. Under mineral nutrient deficiency, the sorghum host secretes large quantities of strigolactones, signalling molecules, into the rhizosphere. These induce S. hermonthica seed germination and subsequent infection of the host roots. In a combination of field and glasshouse experiments, we analysed the effect of microdose applied diammonium hydrogen phosphate (DAP) fertiliser on production of strigolactones, S. hermonthica infection and yield of three different African sorghum genotypes (CGM19 ⁄ 1-1, Lina-3, DouaG). The sorghum cultivars all produced the strigolactones sorgomol and 5-deoxystrigol, albeit in different quantity and ratio. Without fertiliser, high S. hermonthica infection and emergence occurred under both glasshouse and field conditions. DAP application reduced secretion of sorgomol and 5deoxystrigol and reduced S. hermonthica germination (66–70%), emergence (49–73%) and dry biomass (90– 96%) under glasshouse conditions. Under field conditions, DAP microdosing reduced S. hermonthica emergence by 40–84% and increased sorghum grain yield by 47–142%. Thus DAP application reduced secretion of strigolactones into the rhizosphere and S. hermonthica parasitism both under controlled and field conditions. Microdosing of DAP may prove to be an efficient and cost effective option to reduce S. hermonthica damage in sorghum in sub-Saharan Africa, particularly in combination with other control options, such as intercropping, use of organic fertiliser and hand pulling of S. hermonthica at flowering to achieve integrated S. hermonthica management.
Metabolic Responses to Early Nutrition

Abstract Early access to nutrients causes short- and long-term increases in body weight and a higher proportion of breast meat at marketing in both chicks and poults. Utilization of yolk close to hatch is by transport to the circulation and to the gastrointestinal tract. The presence of feed probably increased the latter route. Dramatic increases in size and length of the small intestines occur close to hatch. Growth of the villi and the crypt depth are depressed when feed is withheld. Pancreatic and biliary secretions to the intestine begin before hatch; the amount of secretion per gram exogenous feed intake changes little after hatch. Brush border enzyme activities increase with intestinal mass and exogenous feed intake. Digestion of lipids was high at 4 days whereas starch and N digestion was lower and increased with age. The enhanced growth caused by early feeding may be due to several effects: improved nutritional maturity of the bird, stimulation of the utilization of yolk, increased intestinal development, and long-term metabolic effects.